diff --git a/workflow/snakemake_rules/main_workflow.smk b/workflow/snakemake_rules/main_workflow.smk
index 8228a9927..0fc179070 100644
--- a/workflow/snakemake_rules/main_workflow.smk
+++ b/workflow/snakemake_rules/main_workflow.smk
@@ -198,6 +198,7 @@ rule subsample:
         sequences=_get_unified_alignment,
         metadata=_get_unified_metadata,
         subsampling_scheme = lambda wildcards: config["builds"][wildcards.build_name]["subsampling_scheme"],
+        exclude = config["files"]["exclude"],
         include = config["files"]["include"],
     output:
         sequences = "results/{build_name}/{build_name}_subsampled_sequences.fasta.xz",
@@ -213,6 +214,7 @@ rule subsample:
             --sequences {input.sequences} \
             --metadata {input.metadata} \
             --config {input.subsampling_scheme} \
+            --exclude {input.exclude} \
             --include {input.include} \
             --output-sequences {output.sequences} \
             --output-metadata {output.metadata} 2>&1 | tee {log}