Species of the genus Tabanus Linnaeus (horse flies) are significant pests and vectors transmitting pathogens to economically important animals including cattle. Therefore, knowledge about genetic diversity; a necessity for understanding disease epidemiology, is of paramount importance. However, such information is limited in Thailand, particularly in the northeastern region despite it being a major cattle production area. We examined genetic diversity of three Tabanus species, T. striatus Fabricius and T. megalops Walker, and T. rubidus Wiedemann based on mitochondrial cytochrome oxidase I (COI) sequences. There was relatively high genetic diversity (max. 2.14%) within populations of T. rubidus from northeastern Thailand but no indication of genetic structuring. Phylogenetic relationships between Thai populations and those recorded from Malaysia, India and Bangladesh involved three genetically divergent lineages which possibly represent different but morphologically similar species. High levels of genetic diversity (max. 4.43% and 5.20%) were found within northeastern populations of T. megalops and T. striatus due to the existence of three genetically divergent lineages within these species. However, there was no signal of geographical association of lineages suggesting panmixia within populations. Phylogenetic relationships between specimens obtained in the present study and those recorded from other countries revealed cryptic genetic diversity with three divergent clades. Further study is required to solve this taxonomic complexity of the T. striatus-complex.