We analyzed the Folmer fragment of the mitochondrial COI gene of three closely related species of Semudobia (Diptera: Cecidomyiidae): S. betulae (Winnertz), S. tarda Roskam, and S. skuhravae Roskam. These species form fruit galls on different birch species (Betula, Betulaceae) in the Holarctic Region. In Japan, larvae of S. betulae and S. tarda were collected from the native Japanese birch, B. platyphylla, whereas S. skuhravae was collected from the eastern Palearctic birch, B. ermanii. In the Netherlands, the three species were collected from intermediate forms between the Eurasian endemic birches, B. pendula and B. pubescens. Additional sequences of Canadian and European S. betulae and S. skuhravae were obtained from the Barcode of Life Data system (BOLD). In a maximum likelihood analysis, the individuals of each species formed strongly supported clades, but genetic divergence was high within each clade indicating species complexes. European and Canadian individuals of S. betulae and S. skuhravae each formed a single clade with low intraspecific variation, suggesting that these species were introduced together with their hosts to North America. In contrast, Japanese individuals of the three Semudobia species were remarkably distant from European and Canadian individuals, indicating that they have been isolated genetically for a long period on their native eastern Palearctic and Japanese hosts.