Fairy shrimp are the most divergent taxon of large branchiopod crustaceans and have a worldwide distribution. Yet the diversity and distribution of fairy shrimps in the “Roof of the World” remain poorly known. Here, based on morphology, we identified three species of fairy shrimp ( Branchinecta orientalis , Chirocephalus graziellae and Branchipodopsis affinis ), among 14 fairy-shrimp populations from the Tibetan Plateau, China. Their phylogenetic relationships were verified based on mitochondrial DNA sequences (cytochrome c oxidase subunit I gene) and two nuclear markers (18S ribosomal RNA gene and internal transcribed spacer 2). Syntopy of different species of fairy shrimp was observed. Some haplotypes were shared among populations, and sequences from B. affinis exhibited a star-like pattern in haplotype networks, suggesting a recent rapid expansion. Finally, a high genetic diversity of fairy shrimp was detected on the Tibetan Plateau. Obtained results contribute to a better knowledge of the diversity of high-altitude fairy shrimps.