The genus Ammonia is one of the most common shallow-water benthic foraminifers. Taxonomic identification of Ammonia species, however, is impeded by their great morphologic variability. In the present study, we combined molecular, morphological and ecological data to define two Ammonia species, termed Ammonia sp. 1 and Ammonia sp. 2. We obtained partial large subunit ribosomal DNA (LSU rDNA) sequences from 42 living specimens collected from the Mediterranean Sea, North Atlantic and South Pacific. DNA sequence analysis confirms that Ammonia sp. 1 and Ammonia sp. 2 form two genetically distinct species. Cluster analysis of their morphological characters shows that both species differ by the size of their tests and size of wall perforations. They may also be adapted to different environmental conditions as suggested by differences in their distribution in the Lagoon of Venice.