The genus Ammonia is one of the most common benthic foraminifer of considerable biogeographic importance. The taxonomic status of most of the described species of Ammonia, however, is yet unsettled. In the present study, we used the partial large subunit ribosomal DNA (LSU rDNA) sequences as an alternative approach to distinguish different specimens of Ammonia living in the Lagoon of Venice. We have obtained DNA sequences from 20 living specimens whose tests were examined previously by scanning electron microscopy (SEM). Sequence analysis revealed the presence of two groups, which differ by more than 10.5%. Within each group, the sequence divergence ranges from 0.2 % to 6.9 %. The two groups that can be separated genetically, are called Ammonia sp. 1 and Ammonia sp. 2. Their morphological distinction, however, is problematic. The tests of Ammonia sp. 1 are generally characterized by a more lobate periphery, more elevated dorsal sutures and larger perforations compared to those of Ammonia sp. 2, but none of these characters can be used with certainty for the morphological distinction of both groups.