Culicoides oxystoma Kieffer is a vector of viruses, filarial nematodes and protozoa of the genus Leishmania transmitted to humans and other animals. Understanding genetic diversity, genetic structure and genetic relationships among geographically widespread populations will provide important information related to disease epidemiology. In this study, genetic diversity, genetic structure and genetic relationships between Thai C. oxystoma and those reported from other countries were inferred based on mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 1 (ITS-1) sequences. A high level of genetic diversity was found in C. oxystoma from Thailand. The maximum K2P intraspecific genetic divergence for COI gene and ITS-1 sequences were 4.29% and 6.55%, respectively. Despite high genetic diversity, no significant genetic differentiation was found within the 13 Thai populations. This could be a result of unspecialized habitat requirement of the larval habitat, abundance and continuous distribution of host blood sources, potential for long distance movement with host via trading. Mitochondrial genealogy analysis of the global population of C. oxystoma revealed three (A, B and C) genetically divergent lineages. Specimens from Thailand were included in the main lineage (A) with those from all other countries except those from Senegal that formed lineage B and those of Lineage C that was exclusively found in Bangladesh. The nuclear (ITS-1) genetic markers genealogy indicated that Thai C. oxystoma belong to the same genetic lineage with those from East, South and Southeast Asia which presumably the true C. oxystoma.