diff --git a/CHANGES.md b/CHANGES.md
index 651d5469b..757f5d711 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -12,10 +12,12 @@
 * filter: Improved the speed and memory usage of subsampling with `--group-by` and `--subsample-max-sequences` by caching each record's group during the first pass instead of reading the metadata a second time. [#2018][] @trvrb
 * filter: Improved the speed of computing groups for `--group-by` subsampling by replacing a row-wise pandas apply with a vectorized operation. [#2018][] @trvrb
 * filter: Improved the speed of writing `--output-metadata` by streaming rows instead of building a dictionary per row. [#2018][] @trvrb
+* Improved the error message for unrecognized arguments. [#2028][] @victorlin
 
 [#2014]: https://github.com/nextstrain/augur/issues/2014
 [#2018]: https://github.com/nextstrain/augur/pull/2018
 [#2025]: https://github.com/nextstrain/augur/pull/2025
+[#2028]: https://github.com/nextstrain/augur/issues/2028
 
 ## 34.0.0 (7 July 2026)
 
diff --git a/augur/__init__.py b/augur/__init__.py
index eadbdbd27..2c2e929d1 100644
--- a/augur/__init__.py
+++ b/augur/__init__.py
@@ -14,7 +14,7 @@
 from .debug import DEBUGGING
 from .errors import AugurError
 from .io.print import print_err
-from .argparse_ import HelpFormatter, add_command_subparsers, add_default_command
+from .argparse_ import HelpFormatter, add_command_subparsers, add_default_command, SUBPARSER_ATTRIBUTE
 
 DEFAULT_AUGUR_RECURSION_LIMIT = 10000
 sys.setrecursionlimit(int(os.environ.get("AUGUR_RECURSION_LIMIT") or DEFAULT_AUGUR_RECURSION_LIMIT))
@@ -68,7 +68,18 @@ def make_parser():
 
 
 def run(argv):
-    args = make_parser().parse_args(argv)
+    parser = make_parser()
+    args, extras = parser.parse_known_args(argv)
+
+    # Workaround for <https://github.com/python/cpython/issues/78660>
+    if extras:
+        # Message format copied from ArgumentParser.parse_args()
+        msg = "unrecognized arguments: %s" % " ".join(extras)
+        if subparser := getattr(args, SUBPARSER_ATTRIBUTE, None):
+            subparser.error(msg)
+        else:
+            parser.error(msg)
+
     try:
         return args.__command__.run(args)
     except AugurError as e:
diff --git a/augur/argparse_.py b/augur/argparse_.py
index 2a2d132a1..c4029033e 100644
--- a/augur/argparse_.py
+++ b/augur/argparse_.py
@@ -85,6 +85,8 @@ def add_subparser(parent_subparsers: _SubParsersAction, *args, **kwargs) -> Argu
     return parent_subparsers.add_parser(*args, **kwargs)
 
 
+SUBPARSER_ATTRIBUTE = '__subparser__'
+
 def add_command_subparsers(subparsers, commands, command_attribute='__command__'):
     """
     Add subparsers for each command module.
@@ -109,8 +111,10 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
         subparser = command.register_parser(subparsers)
 
         # Add default attribute for command module
-        if command_attribute:
-            subparser.set_defaults(**{command_attribute: command})
+        subparser.set_defaults(**{command_attribute: command})
+
+        # Add a reference to the subparser
+        subparser.set_defaults(**{SUBPARSER_ATTRIBUTE: subparser})
 
         # Use the same formatting class for every command for consistency.
         # Set here to avoid repeating it in every command's register_parser().