The taxonomic classification within the genus Tritrichomonas is a subject of controversy, and, potentially, separation of the tritrichomonads from cattle and swine on the species level is not valid. To tackle this hypothesis we comparatively assessed several isolates of protozoan parasites from the three Tritrichomonas species T. foetus, T. suis, and T. mobilensis by the RAPD (random amplified polymorphic DNA) technique. In this method with 20 different primers, all T. foetus and T. suis isolates resulted in identical genomic fingerprints, thus yielding additional evidence for the genetic identity of T. foetus and T. suis. In contrast, it turned out that the species T. mobilensis isolated from the squirrel monkey is genetically distinct and can clearly be discriminated from the other tritrichomonads. Consequently, the results obtained in this study support a possible future revision of the taxonomic classification of the genus Tritrichomonas.