AbstractThe phylogenetic relationships of Tephritis Latreille, one of the largest genera of true fruit flies, are poorly understood due to the large number of species, lack of reliable morphological characters and difficulties in identification. In the present study we used two datasets to address these problems: one with 35 species of the genus Tephritis (28 from the Palaearctic and seven from the Nearctic Region) and seven species from closely related genera of the tribe Tephritini (one species each of Actinoptera Rondani, Capitites Foote & Freidberg, Euaresta Loew, Goniurellia Hendel, Trupanea Schrank and two species of Heringina Aczél). For this dataset, we inferred the phylogenetic relationships using five genes (2914 bp): mitochondrial COI (687 bp), mitochondrial 16S rRNA (561 bp), and the nuclear genes Period (481 bp), AATS (444 bp), and the 28S rRNA (741 bp). The second dataset consisted of 64 species of the genus Tephritis, two species of Heringina and one Capitites as an ougtroup and phylogenetic relationships were only inferred using COI (687 bp). The results of both analyses advance the understanding of species relationships, composition of species groups, and existing concepts of homology, relationships and divergence of the genus. Our results based on molecular phylogenetic relationships show that morphological characters are occasionally uninformative for delimiting monophyletic species groups; however, 10 species groups are moderately well supported based on their association with certain host plant taxa (genera, subtribes or tribes). Furthermore, we discuss monophyly of the genus Tephritis, and its relationships with the closely related genera Heringina and Capitites .