Columbids (pigeons and doves) are the primary host of Trichomonas gallinae, the flagellate protozoon which causes avian trichomoniasis, a widespread, often lethal disease. Although predominantly apathogenic, the organism is paradigmatic for the study of strain-specific virulence, with some strains causing greater than 75% mortality and epizootic die-offs in wildlife populations. In recent years, research on this important emerging pathogen has been neglected and genetic variation within the parasite has not hitherto been investigated. The pink pigeon (Columba mayeri), endemic to Mauritius and one of the world's rarest pigeons, suffers high levels of nestling/fledgling mortality from trichomoniasis. As a closed oceanic island population with recorded life-history parameters for all birds, this species represents a unique resource for the study of this host-parasite interaction. To investigate genetic variation within T. gallinae in Mauritian columbids, isolates were collected from pink pigeons and another widespread species, the Madagascar turtle-dove (Streptopelia picturata). Comparison of the 5.8S region of rDNA and surrounding internally transcribed spacer regions (ITS) showed no sequence variation between isolates or with an unrelated but previously sequenced T. gallinae isolate (Genbank). This confirmed all 24 isolates as T. gallinae, and defined this section of the genome as a good species marker. In contrast, Random Amplified Polymorphic DNA (RAPD) analysis of the isolates revealed considerable genotypic variation between isolates. RAPD genotypes appeared to correlate with geographic distribution and host species, suggesting inter-species transmission and rapid host adaptation by the parasite.