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Ulidiidae is a small Tephritoidea family. Ulidiidae are often combined with Otitidae in one family, named Ulidiidae or Otitidae. Our analysis of the genital structures revealed that Ulidiidae + Otitidae form a paraphyletic group, referring to derived Tephritoidea. Therefore, we consider Ulidiidae and Otitidae as separate families. We studied sequences of the COI gene of 58 specimens of 25 species of Ulidiidae and Otitidae. COI was shown to be an effective marker to distinguish Ulidiidae and Otitidae species, except for the genus Melieria (Otitidae). Melieria shows the highest level of intraspecies differences and smallest - of interspecific with high support at all cladograms. This suggests that Melieria is a young genus, being is at the stage of intense speciation. Monophyly of the family Ulidiidae with the inclusion of Homalocephala not confirmed on any of the molecular reconstruction. The position of the genus Homalocephala is indefinite. On the MP and NJ cladograms it forms a sister group to the Otitidae. On the ML and Bayes cladograms Homalocephala species are included in clusters of both families as their basal elements. Our study of genital structures has shown that the genus Homalocephala cannot be included neither in Ulidiidae, nor in Otitidae. It represents the separate clade within the Tephritoidea, which requires further study. In all cladograms genera Timia and Ulidia form mixed cluster. This is consistent with the morphological data on which these genera are very close to each other under the external morphology and genital structures and have little or no hiatus.