diff --git a/snakemake/config.smk b/snakemake/config.smk
index b47ee9b..2f0df30 100644
--- a/snakemake/config.smk
+++ b/snakemake/config.smk
@@ -11,6 +11,45 @@ from typing import Optional
 from textwrap import dedent, indent
 
 
+# Set search paths for Augur
+if "AUGUR_SEARCH_PATHS" in os.environ:
+    print(dedent(f"""\
+        Using existing search paths in AUGUR_SEARCH_PATHS:
+
+            {os.environ["AUGUR_SEARCH_PATHS"]!r}
+        """), file=sys.stderr)
+else:
+    # Note that this differs from the search paths used in
+    # resolve_config_path().
+    # This is the preferred default moving forwards, and the plan is to
+    # eventually update resolve_config_path() to use AUGUR_SEARCH_PATHS.
+    search_paths = [
+        # User analysis directory
+        Path.cwd(),
+
+        # Workflow defaults folder
+        Path(workflow.basedir) / "defaults",
+
+        # Workflow root (contains Snakefile)
+        Path(workflow.basedir),
+    ]
+
+    # This should work for majority of workflows, but we could consider doing a
+    # more thorough search for the nextstrain-pathogen.yaml. This would likely
+    # replicate how CLI searches for the root.¹
+    # ¹ <https://github.com/nextstrain/cli/blob/d5e184c5/nextstrain/cli/command/build.py#L413-L420>
+    repo_root = Path(workflow.basedir) / ".."
+    if (repo_root / "nextstrain-pathogen.yaml").is_file():
+        search_paths.extend([
+            # Pathogen repo root
+            repo_root,
+        ])
+
+    search_paths = [path.resolve() for path in search_paths if path.is_dir()]
+
+    os.environ["AUGUR_SEARCH_PATHS"] = ":".join(map(str, search_paths))
+
+
 class InvalidConfigError(Exception):
     pass