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Fasciolosis, a food- and waterborne infection caused by the trematodes Fasciola hepatica and F. gigantica, is recognized by WHO as a neglected zoonotic disease. Whereas F. hepatica is distributed worldwide in cooler climates, F. gigantica occurs mainly in the tropics of Africa and Asia. The southern Caucasus, with Armenia, is one of the most northern regions where both species occur and may produce hybrids. In this study, livestock in central Armenia was surveyed for fasciolosis, the causative species were determined and the genetic diversity of both species was estimated. Total prevalence in sheep (1794), cattle (324) and goats (9) was 21.2%, 15.7% and 44.4%, respectively. After morphological identification and sequencing of a mitochondrial (nad1) and a nuclear marker gene (28S rRNA), 62 collected specimens were allocated to F. hepatica (n = 55) and F. gigantica (n = 7). Intraspecific diversity was evaluated for the complete nad1 gene, resulting in 29 haplotypes of F. hepatica and six haplotypes of F. gigantica. Diversity was higher among F. gigantica than F. hepatica in the Armenian sample set, a difference that was confirmed analyzing available sequences for both species worldwide. Maximum genetic distance between haplotypes in global networks was 49 nucleotide steps for F. gigantica compared to 15 for F. hepatica. In the available sample sets, F. hepatica showed higher diversity in western Asia and the Middle East compared to Europe and eastern Asia, while for F. gigantica loosely structured clusters comprising mainly western/southern Asian and African haplotypes could be identified. A distinct clade comprising haplotypes from Zambia was basal in the phylogenetic tree. Biogeographical implications of these data are discussed.