To help resolve phylogenetic relationships among bisexual Artemia populations, phylogenetic analysis was conducted using DNA sequences from the nuclear DNA internal transcribed spacer 1 (ITS-1) and portions of the mitochondrial genome corresponding to the cytochrome oxidase I (COI). DNA sequences were generated for nine bisexual Artemia populations living in different regions of the world. Phylogenetic trees based on ITS-1 and COI sequences indicated that bisexual Artemia populations consist of four groups. The bisexual Artemia populations from Tibet and Kazakstan always clustered with Artemia urmiana in the same group; there is small sequence divergence and genetic distance among them. Therefore, we deduced that bisexual Artemia populations from Tibet and Kazakstan may belong to the A. urmiana group. Our study did not support that bisexual Artemia populations from Tibet are a new, separate species A. tibetiana. We also found that A. sinica and A. urmiana have a small genetic distance. Based upon these findings, we conclude that A. urmiana may have played an important role in the evolution of A. sinica.