diff --git a/CHANGES.md b/CHANGES.md
index d96eaead..3f09f244 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -15,6 +15,8 @@ development source code and as such may not be routinely kept up to date.
 
 ## Improvements
 
+* `nextstrain setup --list` now lists the available pathogens for setup.
+  ([#502](https://github.com/nextstrain/cli/issues/502)
 * Added the following to the list of "well-known" environment variables that are
   automatically passed thru to runtimes:
 
diff --git a/doc/changes.md b/doc/changes.md
index 0480819d..0b42c0c6 100644
--- a/doc/changes.md
+++ b/doc/changes.md
@@ -19,6 +19,8 @@ development source code and as such may not be routinely kept up to date.
 (v-next-improvements)=
 ### Improvements
 
+* `nextstrain setup --list` now lists the available pathogens for setup.
+  ([#502](https://github.com/nextstrain/cli/issues/502)
 * Added the following to the list of "well-known" environment variables that are
   automatically passed thru to runtimes:
 
diff --git a/doc/commands/setup.rst b/doc/commands/setup.rst
index 9c32b595..03bcb46a 100644
--- a/doc/commands/setup.rst
+++ b/doc/commands/setup.rst
@@ -14,6 +14,7 @@ nextstrain setup
 
     usage: nextstrain setup [--dry-run] [--force] [--set-default] <pathogen-name>[@<version>[=<url>]]
            nextstrain setup [--dry-run] [--force] [--set-default] <runtime-name>
+           nextstrain setup --list
            nextstrain setup --help
 
 
@@ -78,3 +79,7 @@ options
 
     Use this pathogen version or runtime as the default if set up is successful.
 
+.. option:: --list
+
+    List available pathogens.
+
diff --git a/nextstrain/cli/command/setup.py b/nextstrain/cli/command/setup.py
index 29cf051e..2fc4e248 100644
--- a/nextstrain/cli/command/setup.py
+++ b/nextstrain/cli/command/setup.py
@@ -24,7 +24,7 @@
 from ..errors import UserError
 from ..util import colored, runner_module, runner_name, print_and_check_setup_tests
 from ..types import Options, RunnerModule, SetupTestResults
-from ..pathogens import PathogenVersion, pathogen_defaults
+from ..pathogens import PathogenVersion, pathogen_defaults, fetch_nextstrain_run_pathogens
 from ..runner import all_runners_by_name, runner_defaults
 
 
@@ -33,10 +33,35 @@
 failure = partial(colored, "red")
 
 
+def list_available_pathogens():
+    """
+    Fetches and displays available pathogens with workflow compatibility details.
+    """
+    print("Fetching available pathogens…")
+    print()
+
+    pathogens = fetch_nextstrain_run_pathogens()
+    pathogens = sorted(pathogens, key=lambda p: p["name"].lower())
+
+    for pathogen in pathogens:
+        print(pathogen["name"])
+
+        compatible_workflows = [
+            workflow
+            for workflow, workflow_info in pathogen.get("registration", {}).get("workflows", {}).items()
+            if isinstance(workflow_info, dict) and workflow_info.get("compatibility", {}).get("nextstrain run")
+        ]
+        if compatible_workflows:
+            print("  Workflows compatible with nextstrain run:")
+            for workflow in compatible_workflows:
+                print(f"    - {workflow}")
+
+
 def register_parser(subparser):
     """
     %(prog)s [--dry-run] [--force] [--set-default] <pathogen-name>[@<version>[=<url>]]
     %(prog)s [--dry-run] [--force] [--set-default] <runtime-name>
+    %(prog)s --list
     %(prog)s --help
     """
     parser = subparser.add_parser("setup", help = "Set up a pathogen or runtime")
@@ -60,7 +85,9 @@ def register_parser(subparser):
 
             A runtime is one of {{{', '.join(all_runners_by_name)}}}.
             """),
-        metavar = "<pathogen>|<runtime>")
+        metavar = "<pathogen>|<runtime>",
+        nargs   = "?",
+        default = None)
 
     parser.add_argument(
         "--dry-run",
@@ -78,11 +105,24 @@ def register_parser(subparser):
         help   = "Use this pathogen version or runtime as the default if set up is successful.",
         action = "store_true")
 
+    parser.add_argument(
+        "--list",
+        help   = "List available pathogens.",
+        action = "store_true")
+
     return parser
 
 
 @console.auto_dry_run_indicator()
 def run(opts: Options) -> int:
+    if opts.list:
+        list_available_pathogens()
+        return 0
+
+    if not opts.arg:
+        print("No pathogen or runtime specified. Run with --list to see available pathogens.")
+        return 1
+
     try:
         runner = runner_module(opts.arg)
     except ValueError as e1:
diff --git a/nextstrain/cli/pathogens.py b/nextstrain/cli/pathogens.py
index d1e2ed81..8d5209c6 100644
--- a/nextstrain/cli/pathogens.py
+++ b/nextstrain/cli/pathogens.py
@@ -1198,3 +1198,33 @@ def nextstrain_repo_zip_url(name: str, version: str) -> URL:
             return URL(urlquote(revision), version_url)
         else:
             return version_url
+
+
+def fetch_nextstrain_run_pathogens() -> List[Dict]:
+    """
+    Fetches all pathogen repos from nextstrain.org, filtered to only those
+    with at least one `nextstrain run` compatible workflow.
+
+    Returns a list of dicts with "name" and optionally "registration" keys.
+    """
+    url = URL("/pathogen-repos", NEXTSTRAIN_DOT_ORG)
+
+    with requests.Session() as http:
+        response = http.get(str(url), headers={"Accept": "application/json"})
+        response.raise_for_status()
+        return [repo for repo in response.json() if has_nextstrain_run_compatibility(repo)]
+
+
+def has_nextstrain_run_compatibility(repo: Dict) -> bool:
+    """
+    Returns True if the pathogen repo has at least one workflow with `nextstrain run` compatibility.
+    """
+    workflows = repo.get("registration", {}).get("workflows", {})
+
+    for workflow in workflows.values():
+        if isinstance(workflow, dict):
+            compatibility = workflow.get("compatibility", {})
+            if compatibility.get("nextstrain run"):
+                return True
+
+    return False