diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d039e25..e4ecfc54 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -71,6 +71,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#164](https://github.com/nf-core/references/pull/164) - Replace `update_references_file` string rewriting with nf-schema `allowParamsSubstitution`, so datasheets can carry `${params.references_base_path}` placeholders
 - [#165](https://github.com/nf-core/references/pull/165) - Document `--references_base_path`, multiple genomes, and the asset file format in `docs/usage.md`
 - [#166](https://github.com/nf-core/references/pull/166) - Rename the datasheet `source`, `source_version`, and derived `source_vcf` meta fields to `reference_source`, `annotation_version`, and `annotation_source` (#65)
+- [#167](https://github.com/nf-core/references/pull/167) - Document reference selection precedence for consuming pipelines in `docs/usage.md`
 
 ### Removed
 
diff --git a/docs/usage.md b/docs/usage.md
index 3b7c697a..ff079a73 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -388,3 +388,14 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+## Reference selection in consuming pipelines
+
+A pipeline that consumes these references resolves each key, such as `fasta` or `fasta_fai`, separately. Each key takes its value from the first source in this order that supplies it:
+
+1. Explicit parameters, for example `--fasta` and `--fasta_fai`.
+2. One references datasheet or one iGenomes catalogue entry. The datasheet is passed as a file, or located from a base URL plus a genome key. Selecting both a datasheet and a catalogue entry is an error.
+
+An explicit `--fasta` with no `--fasta_fai` therefore takes `fasta_fai` from the datasheet or catalogue entry.
+
+Each consuming pipeline names its own parameters for these sources and documents them in its usage pages. See the [nf-core/bamtofastq usage documentation](https://nf-co.re/bamtofastq/usage) for an example.