diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
index 0de1de0e8cd..f7da3d219f5 100644
--- a/modules/nf-core/blast/blastn/main.nf
+++ b/modules/nf-core/blast/blastn/main.nf
@@ -10,6 +10,9 @@ process BLAST_BLASTN {
     input:
     tuple val(meta) , path(fasta)
     tuple val(meta2), path(db)
+    path taxidlist
+    val taxids
+    val negative_tax
 
     output:
     tuple val(meta), path('*.txt'), emit: txt
@@ -23,6 +26,12 @@ process BLAST_BLASTN {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.getExtension() == "gz" ? true : false
     def fasta_name = is_compressed ? fasta.getBaseName() : fasta
+    def negative_tax_cmd = negative_tax ? "negative_" : ""
+    def taxidlist_cmd = taxidlist ? "-${negative_tax_cmd}taxidlist ${taxidlist}" : ""
+    def taxids_cmd = taxids ? "-${negative_tax_cmd}taxids ${taxids}" : ""
+    if (taxidlist_cmd.any() && taxids_cmd.any()) {
+        log.error("ERROR: taxidlist and taxids can not be used at the same time, choose only one argument to use for tax id filtering.")
+    }
 
     """
     if [ "${is_compressed}" == "true" ]; then
@@ -39,6 +48,8 @@ process BLAST_BLASTN {
         -num_threads ${task.cpus} \\
         -db \$DB \\
         -query ${fasta_name} \\
+        ${taxidlist_cmd} \\
+        ${taxids_cmd} \\
         ${args} \\
         -out ${prefix}.txt
 
diff --git a/modules/nf-core/blast/blastn/tests/main.nf.test b/modules/nf-core/blast/blastn/tests/main.nf.test
index aacc93c5d7c..f11796fcc32 100644
--- a/modules/nf-core/blast/blastn/tests/main.nf.test
+++ b/modules/nf-core/blast/blastn/tests/main.nf.test
@@ -31,6 +31,9 @@ nextflow_process {
                 """
                 input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
                 input[1] = BLAST_MAKEBLASTDB.out.db
+                input[2] = []
+                input[3] = []
+                input[4] = []
                 """
             }
         }
@@ -55,6 +58,9 @@ nextflow_process {
                 """
                 input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ]
                 input[1] = BLAST_MAKEBLASTDB.out.db
+                input[2] = []
+                input[3] = []
+                input[4] = []
                 """
             }
         }
diff --git a/modules/nf-core/blast/blastn/tests/main.nf.test.snap b/modules/nf-core/blast/blastn/tests/main.nf.test.snap
index 348a6f5fa89..3b6703866e0 100644
--- a/modules/nf-core/blast/blastn/tests/main.nf.test.snap
+++ b/modules/nf-core/blast/blastn/tests/main.nf.test.snap
@@ -7,9 +7,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-01T11:32:43.169365323"
+        "timestamp": "2025-08-04T14:26:27.847166"
     },
     "versions_zipped": {
         "content": [
@@ -19,8 +19,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "24.10.6"
         },
-        "timestamp": "2025-04-01T11:32:48.452742327"
+        "timestamp": "2025-08-04T14:52:40.954652"
     }
 }
\ No newline at end of file