diff --git a/README.md b/README.md
index 4ecaf4d..0c024df 100644
--- a/README.md
+++ b/README.md
@@ -333,6 +333,8 @@ The `--file-key` argument is passed the `test` key name from the `files` configu
 
 The `--file-key`, `--output`, and `--matrix` flags must be used together. `--matrix` may be an empty string if the file that should be generated does not depend on any specific matrix variations.
 
+Where multiple values for the same key are passed to `--matrix`, e.g. `cuda_suffixed=true;cuda_suffixed=false`, only the last value will be used.
+
 The `--prepend-channel` argument accepts additional channels to use, like `rapids-dependency-file-generator --prepend-channel my_channel --prepend-channel my_other_channel`.
 If both `--output` and `--prepend-channel` are provided, the output format must be conda.
 Prepending channels can be useful for adding local channels with packages to be tested in CI workflows.
diff --git a/tests/test_cli.py b/tests/test_cli.py
index f41091d..a5c2944 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -11,6 +11,16 @@ def test_generate_matrix():
     assert matrix is None
 
 
+def test_generate_matrix_allows_duplicates_and_chooses_the_final_value():
+    # duplicate keys
+    matrix = generate_matrix("thing=abc;other_thing=true;thing=def;thing=ghi")
+    assert matrix == {"other_thing": ["true"], "thing": ["ghi"]}
+
+    # duplicate keys and values
+    matrix = generate_matrix("thing=abc;thing=abc")
+    assert matrix == {"thing": ["abc"]}
+
+
 def test_validate_args():
     # Missing output
     with pytest.raises(Exception):
@@ -106,3 +116,17 @@ def test_validate_args():
             "my_other_channel",
         ]
     )
+
+    # Valid, with duplicates in --matrix
+    validate_args(
+        [
+            "-c",
+            "dependencies2.yaml",
+            "--output",
+            "pyproject",
+            "--matrix",
+            "cuda_suffixed=true;arch=x86_64;cuda_suffixed=false",
+            "--file-key",
+            "all",
+        ]
+    )