diff --git a/noodles-bam/Cargo.toml b/noodles-bam/Cargo.toml
index 06b8204da..b134bcd7e 100644
--- a/noodles-bam/Cargo.toml
+++ b/noodles-bam/Cargo.toml
@@ -18,6 +18,7 @@ bit-vec.workspace = true
 byteorder.workspace = true
 bytes.workspace = true
 futures = { workspace = true, optional = true, features = ["std"] }
+indexmap.workspace = true
 tokio = { workspace = true, optional = true, features = ["fs", "io-util"] }
 
 noodles-bgzf = { path = "../noodles-bgzf", version = "0.25.0" }
diff --git a/noodles-bam/src/bai/async/reader.rs b/noodles-bam/src/bai/async/reader.rs
index aed6f2eaf..194a6e6fc 100644
--- a/noodles-bam/src/bai/async/reader.rs
+++ b/noodles-bam/src/bai/async/reader.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::{
     index::{
@@ -144,7 +143,7 @@ where
     Ok(ReferenceSequence::new(bins, intervals, metadata))
 }
 
-async fn read_bins<R>(reader: &mut R) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+async fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: AsyncRead + Unpin,
 {
@@ -152,7 +151,7 @@ where
 
     const METADATA_ID: usize = Bin::metadata_id(DEPTH);
 
-    fn duplicate_bin_error(id: usize) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)> {
+    fn duplicate_bin_error(id: usize) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)> {
         Err(io::Error::new(
             io::ErrorKind::InvalidData,
             format!("duplicate bin ID: {id}"),
@@ -163,7 +162,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
     let mut metadata = None;
 
     for _ in 0..n_bin {
diff --git a/noodles-bam/src/bai/async/writer.rs b/noodles-bam/src/bai/async/writer.rs
index 53c731866..64c6c96c2 100644
--- a/noodles-bam/src/bai/async/writer.rs
+++ b/noodles-bam/src/bai/async/writer.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::index::{
     reference_sequence::{bin::Chunk, Bin, Metadata},
@@ -163,7 +162,7 @@ where
 
 async fn write_bins<W>(
     writer: &mut W,
-    bins: &HashMap<usize, Bin>,
+    bins: &IndexMap<usize, Bin>,
     metadata: Option<&Metadata>,
 ) -> io::Result<()>
 where
diff --git a/noodles-bam/src/bai/reader.rs b/noodles-bam/src/bai/reader.rs
index 63ff79f7e..18bc48609 100644
--- a/noodles-bam/src/bai/reader.rs
+++ b/noodles-bam/src/bai/reader.rs
@@ -1,9 +1,7 @@
-use std::{
-    collections::HashMap,
-    io::{self, Read},
-};
+use std::io::{self, Read};
 
 use byteorder::{LittleEndian, ReadBytesExt};
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::{
     index::{
@@ -141,7 +139,7 @@ where
     Ok(references)
 }
 
-fn read_bins<R>(reader: &mut R) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: Read,
 {
@@ -149,7 +147,7 @@ where
 
     const METADATA_ID: usize = Bin::metadata_id(DEPTH);
 
-    fn duplicate_bin_error(id: usize) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)> {
+    fn duplicate_bin_error(id: usize) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)> {
         Err(io::Error::new(
             io::ErrorKind::InvalidData,
             format!("duplicate bin ID: {id}"),
@@ -160,7 +158,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
     let mut metadata = None;
 
     for _ in 0..n_bin {
diff --git a/noodles-csi/CHANGELOG.md b/noodles-csi/CHANGELOG.md
index 8e61f4b8c..6df690711 100644
--- a/noodles-csi/CHANGELOG.md
+++ b/noodles-csi/CHANGELOG.md
@@ -1,5 +1,17 @@
 # Changelog
 
+## Unreleased
+
+### Changed
+
+  * csi/index/reference_sequence: Change bins to an ordered map ([#213]).
+
+    Bins now maintain their insertion order. While this does not directly
+    affect reading and in-memory usage, it does make serialization
+    deterministic.
+
+[#213]: https://github.com/zaeleus/noodles/issues/213
+
 ## 0.25.1 - 2023-10-19
 
 ### Fixed
diff --git a/noodles-csi/src/async/reader.rs b/noodles-csi/src/async/reader.rs
index 4a1c11e79..e9ca790f2 100644
--- a/noodles-csi/src/async/reader.rs
+++ b/noodles-csi/src/async/reader.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use tokio::io::{self, AsyncRead, AsyncReadExt};
 
@@ -176,7 +175,7 @@ where
 async fn read_bins<R>(
     reader: &mut R,
     depth: u8,
-) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: AsyncRead + Unpin,
 {
@@ -184,7 +183,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
 
     let metadata_id = Bin::metadata_id(depth);
     let mut metadata = None;
diff --git a/noodles-csi/src/async/writer.rs b/noodles-csi/src/async/writer.rs
index 747d83163..ccdaa8509 100644
--- a/noodles-csi/src/async/writer.rs
+++ b/noodles-csi/src/async/writer.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use tokio::io::{self, AsyncWrite, AsyncWriteExt};
 
@@ -183,7 +182,7 @@ where
 async fn write_bins<W>(
     writer: &mut W,
     depth: u8,
-    bins: &HashMap<usize, Bin>,
+    bins: &IndexMap<usize, Bin>,
     metadata: Option<&Metadata>,
 ) -> io::Result<()>
 where
diff --git a/noodles-csi/src/index/reference_sequence.rs b/noodles-csi/src/index/reference_sequence.rs
index 76980c129..316e591e9 100644
--- a/noodles-csi/src/index/reference_sequence.rs
+++ b/noodles-csi/src/index/reference_sequence.rs
@@ -6,9 +6,10 @@ mod metadata;
 
 pub use self::{bin::Bin, builder::Builder, metadata::Metadata};
 
-use std::{collections::HashMap, io, num::NonZeroUsize};
+use std::{io, num::NonZeroUsize};
 
 use bit_vec::BitVec;
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_core::{region::Interval, Position};
 
@@ -21,7 +22,7 @@ const LINEAR_INDEX_WINDOW_SIZE: usize = 1 << 14;
 /// A CSI reference sequence.
 #[derive(Clone, Debug, Eq, PartialEq)]
 pub struct ReferenceSequence {
-    bins: HashMap<usize, Bin>,
+    bins: IndexMap<usize, Bin>,
     linear_index: Vec<bgzf::VirtualPosition>,
     metadata: Option<Metadata>,
 }
@@ -42,7 +43,7 @@ impl ReferenceSequence {
     /// let reference_sequence = ReferenceSequence::new(Default::default(), Vec::new(), None);
     /// ```
     pub fn new(
-        bins: HashMap<usize, Bin>,
+        bins: IndexMap<usize, Bin>,
         linear_index: Vec<bgzf::VirtualPosition>,
         metadata: Option<Metadata>,
     ) -> Self {
@@ -64,7 +65,7 @@ impl ReferenceSequence {
     /// let reference_sequence = ReferenceSequence::new(Default::default(), Vec::new(), None);
     /// assert!(reference_sequence.bins().is_empty());
     /// ```
-    pub fn bins(&self) -> &HashMap<usize, Bin> {
+    pub fn bins(&self) -> &IndexMap<usize, Bin> {
         &self.bins
     }
 
diff --git a/noodles-csi/src/index/reference_sequence/builder.rs b/noodles-csi/src/index/reference_sequence/builder.rs
index d991177b9..35e0e9527 100644
--- a/noodles-csi/src/index/reference_sequence/builder.rs
+++ b/noodles-csi/src/index/reference_sequence/builder.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_core::Position;
 
@@ -11,7 +10,7 @@ use super::{
 /// A CSI reference sequence builder.
 #[derive(Debug)]
 pub struct Builder {
-    bin_builders: HashMap<usize, bin::Builder>,
+    bin_builders: IndexMap<usize, bin::Builder>,
     linear_index: Vec<Option<bgzf::VirtualPosition>>,
     start_position: bgzf::VirtualPosition,
     end_position: bgzf::VirtualPosition,
@@ -128,7 +127,7 @@ impl Builder {
 impl Default for Builder {
     fn default() -> Self {
         Self {
-            bin_builders: HashMap::new(),
+            bin_builders: IndexMap::new(),
             linear_index: Vec::new(),
             start_position: bgzf::VirtualPosition::MAX,
             end_position: bgzf::VirtualPosition::MIN,
@@ -226,11 +225,7 @@ mod tests {
             ReferenceSequence::new(bins, linear_index, Some(metadata))
         };
 
-        for (id, expected_bin) in expected.bins() {
-            let actual_bin = actual.bins().get(id).expect("missing bin");
-            assert_eq!(actual_bin, expected_bin);
-        }
-
+        assert_eq!(actual.bins(), expected.bins());
         assert_eq!(actual.linear_index(), expected.linear_index());
         assert_eq!(actual.metadata(), expected.metadata());
 
diff --git a/noodles-csi/src/reader.rs b/noodles-csi/src/reader.rs
index d617bdec1..b33345585 100644
--- a/noodles-csi/src/reader.rs
+++ b/noodles-csi/src/reader.rs
@@ -1,10 +1,10 @@
 use std::{
-    collections::HashMap,
     io::{self, Read},
     str,
 };
 
 use byteorder::{LittleEndian, ReadBytesExt};
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 
 use super::{
@@ -234,11 +234,11 @@ where
     Ok(ReferenceSequence::new(bins, Vec::new(), metadata))
 }
 
-fn read_bins<R>(reader: &mut R, depth: u8) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+fn read_bins<R>(reader: &mut R, depth: u8) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: Read,
 {
-    fn duplicate_bin_error(id: usize) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)> {
+    fn duplicate_bin_error(id: usize) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)> {
         Err(io::Error::new(
             io::ErrorKind::InvalidData,
             format!("duplicate bin ID: {id}"),
@@ -249,7 +249,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
 
     let metadata_id = Bin::metadata_id(depth);
     let mut metadata = None;
diff --git a/noodles-csi/src/writer.rs b/noodles-csi/src/writer.rs
index ac280f1eb..82e152400 100644
--- a/noodles-csi/src/writer.rs
+++ b/noodles-csi/src/writer.rs
@@ -1,9 +1,7 @@
-use std::{
-    collections::HashMap,
-    io::{self, Write},
-};
+use std::io::{self, Write};
 
 use byteorder::{LittleEndian, WriteBytesExt};
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 
 use super::{
@@ -183,7 +181,7 @@ where
 fn write_bins<W>(
     writer: &mut W,
     depth: u8,
-    bins: &HashMap<usize, Bin>,
+    bins: &IndexMap<usize, Bin>,
     metadata: Option<&Metadata>,
 ) -> io::Result<()>
 where
diff --git a/noodles-tabix/Cargo.toml b/noodles-tabix/Cargo.toml
index 381aae616..cfe2515f3 100644
--- a/noodles-tabix/Cargo.toml
+++ b/noodles-tabix/Cargo.toml
@@ -16,6 +16,7 @@ async = ["dep:tokio", "noodles-bgzf/async"]
 [dependencies]
 bit-vec.workspace = true
 byteorder.workspace = true
+indexmap.workspace = true
 noodles-bgzf = { path = "../noodles-bgzf", version = "0.25.0" }
 noodles-core = { path = "../noodles-core", version = "0.12.0" }
 noodles-csi = { path = "../noodles-csi", version = "0.25.1" }
diff --git a/noodles-tabix/src/async/reader.rs b/noodles-tabix/src/async/reader.rs
index ff3a853fe..481ccd34a 100644
--- a/noodles-tabix/src/async/reader.rs
+++ b/noodles-tabix/src/async/reader.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::index::{
     header::{Format, ReferenceSequenceNames},
@@ -230,7 +229,7 @@ where
     Ok(ReferenceSequence::new(bins, intervals, metadata))
 }
 
-async fn read_bins<R>(reader: &mut R) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+async fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: AsyncRead + Unpin,
 {
@@ -242,7 +241,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
     let mut metadata = None;
 
     for _ in 0..n_bin {
diff --git a/noodles-tabix/src/async/writer.rs b/noodles-tabix/src/async/writer.rs
index d82f5bf93..e5df074a6 100644
--- a/noodles-tabix/src/async/writer.rs
+++ b/noodles-tabix/src/async/writer.rs
@@ -1,5 +1,4 @@
-use std::collections::HashMap;
-
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::index::{
     header::ReferenceSequenceNames,
@@ -220,7 +219,7 @@ where
 
 async fn write_bins<W>(
     writer: &mut W,
-    bins: &HashMap<usize, Bin>,
+    bins: &IndexMap<usize, Bin>,
     metadata: Option<&Metadata>,
 ) -> io::Result<()>
 where
diff --git a/noodles-tabix/src/reader.rs b/noodles-tabix/src/reader.rs
index e4ce5549b..109455a66 100644
--- a/noodles-tabix/src/reader.rs
+++ b/noodles-tabix/src/reader.rs
@@ -1,11 +1,10 @@
 use std::{
-    collections::HashMap,
     io::{self, Read},
     str,
 };
 
-use super::MAGIC_NUMBER;
 use byteorder::{LittleEndian, ReadBytesExt};
+use indexmap::IndexMap;
 use noodles_bgzf as bgzf;
 use noodles_csi::{
     index::{
@@ -16,6 +15,8 @@ use noodles_csi::{
     Index,
 };
 
+use super::MAGIC_NUMBER;
+
 const NUL: u8 = b'\x00';
 
 /// A tabix reader.
@@ -236,7 +237,7 @@ where
     Ok(references)
 }
 
-fn read_bins<R>(reader: &mut R) -> io::Result<(HashMap<usize, Bin>, Option<Metadata>)>
+fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
 where
     R: Read,
 {
@@ -248,7 +249,7 @@ where
         usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
     })?;
 
-    let mut bins = HashMap::with_capacity(n_bin);
+    let mut bins = IndexMap::with_capacity(n_bin);
     let mut metadata = None;
 
     for _ in 0..n_bin {