diff --git a/rescript/plugin_setup.py b/rescript/plugin_setup.py
index 8eae397..17ea965 100644
--- a/rescript/plugin_setup.py
+++ b/rescript/plugin_setup.py
@@ -1056,15 +1056,16 @@
         'primer_fwd': Str,
         'primer_rev': Str,
         'position_start': Int % Range(1, None),
-        'position_end': Int % Range(1, None)
+        'position_end': Int % Range(1, None),
+        'n_threads': Int % Range(1, None),
     },
     outputs=[('trimmed_sequences', FeatureData[AlignedSequence]), ],
     input_descriptions={'aligned_sequences': 'Aligned DNA sequences.', },
     parameter_descriptions={
         'primer_fwd': 'Forward primer used to find the start position '
-                      'for alignment trimming.',
+                      'for alignment trimming. Provide as 5\'-3\'.',
         'primer_rev': 'Reverse primer used to find the end position '
-                      'for alignment trimming.',
+                      'for alignment trimming. Provide as 5\'-3\'.',
         'position_start': 'Position within the alignment where the trimming '
                           'will begin. If not provided, alignment will not'
                           'be trimmed at the beginning. If forward primer is'
@@ -1072,7 +1073,10 @@
         'position_end': 'Position within the alignment where the trimming '
                         'will end. If not provided, alignment will not be '
                         'trimmed at the end. If reverse primer is specified '
-                        'this parameter will be ignored.'
+                        'this parameter will be ignored.',
+        'n_threads': 'Number of threads to use for primer-based trimming, '
+                     'otherwise ignored. (Use `auto` to automatically use '
+                     'all available cores)'
     },
     output_descriptions={
         'trimmed_sequences': 'Trimmed sequence alignment.', },
diff --git a/rescript/trim_alignment.py b/rescript/trim_alignment.py
index 297be24..da9f1de 100644
--- a/rescript/trim_alignment.py
+++ b/rescript/trim_alignment.py
@@ -190,11 +190,13 @@ def _trim_alignment(expand_alignment_action,
                     primer_fwd=None,
                     primer_rev=None,
                     position_start=None,
-                    position_end=None) -> AlignedDNAFASTAFormat:
+                    position_end=None,
+                    n_threads=1) -> AlignedDNAFASTAFormat:
     """
     Trim alignment based on primer alignment or explicitly specified
     positions. When at least one primer sequence is given, primer-based
-    trimming will be performed, otherwise position-based trimming is done.
+    trimming will be performed via the `addfragments` option of mafft,
+    otherwise position-based trimming is done.
 
     Arguments:
         expand_alignment_action: qiime action for multiple seq. alignment
@@ -222,7 +224,8 @@ def _trim_alignment(expand_alignment_action,
         alignment_with_primers, = expand_alignment_action(
             alignment=aligned_sequences,
             sequences=primers,
-            addfragments=True)
+            addfragments=True,
+            n_threads=n_threads)
 
         # find trim positions based on primer positions within alignment
         trim_positions = _locate_primer_positions(alignment_with_primers)
@@ -244,7 +247,8 @@ def trim_alignment(ctx,
                    primer_fwd=None,
                    primer_rev=None,
                    position_start=None,
-                   position_end=None):
+                   position_end=None,
+                   n_threads=1):
     """
     Trim an existing alignment based on provided primers or specific,
     pre-defined positions. Primers take precedence over the positions,
@@ -263,6 +267,7 @@ def trim_alignment(ctx,
         primer_fwd,
         primer_rev,
         position_start,
-        position_end)
+        position_end,
+        n_threads=n_threads)
 
     return qiime2.Artifact.import_data('FeatureData[AlignedSequence]', result)