diff --git a/src/msapll.cpp b/src/msapll.cpp
index 3773456..d084829 100644
--- a/src/msapll.cpp
+++ b/src/msapll.cpp
@@ -516,8 +516,9 @@ namespace modeltest
 
           /* read FASTA sequences for finding the number of tips and seq len */
           /* make sure they are all of the same length */
+          int ret;
           for (cur_seq = 0;
-               pll_fasta_getnext (fp, &hdr, &hdr_len, &seq, &n_sites_read, &seq_idx); ++cur_seq)
+               (ret = pll_fasta_getnext (fp, &hdr, &hdr_len, &seq, &n_sites_read, &seq_idx)); ++cur_seq)
           {
               if (dt_unknown)
               {
@@ -557,6 +558,14 @@ namespace modeltest
               free (hdr);
           }
 
+          // Passthrough illegal character errors
+          if (ret == PLL_FAILURE && (pll_errno == PLL_ERROR_FASTA_ILLEGALCHAR || pll_errno == PLL_ERROR_FASTA_UNPRINTABLECHAR)) {
+              mt_errno = MT_ERROR_ALIGNMENT;
+              strncpy(mt_errmsg, pll_errmsg, ERR_MSG_SIZE);
+              free(hdr);
+              free(seq);
+          }
+
           if (sites == MT_SIZE_UNDEF)
           {
               switch (pll_errno)