Objective To investigate the effect and expression regulation of hypoxia-inducible factor alpha (Hif-α) for schizothoracine fish under hypoxic environment. Methods We obtained the coding regions of Hif-1αΑ, Hif-1αB,Hif-2αΑ, and Hif-2αB genes for 13 species of schizothoracine fish, endemic to the Qinghai-Tibetan Plateau, using RTPCR,then conducted molecular evolution analysis based on the schizothoracine fish phylogeny by comparing the nonsynonymous/synonymous substitution ratios. Gymnocypris eckloni was selected to investigate the tissue expression patterns inresponse to hypoxia. Results The coding regions of Hif-1αΑ, Hif-1αB, Hif-2αΑ, and Hif-2αB genes were 2196 bp, 2325bp, 2544 bp, and 2511 bp in length, respectively. Sequence alignment showed that the conserved proline hydroxylationmotif LxxLAP was deletion in the NODD domain of HIF-1αΑ in schizothoracine fish, and the mutation from the prolinehydroxylation motif to PxxLAP was observed in the CODD domain of HIF-1αB in the specialized and highly specializedschizothoracine fish. Under severe hypoxic conditions, the expression of Hif-α gene in the brain and heart of G. ecklonidecreased significantly compared to normoxia control. Under moderate hypoxic conditions, the expression of Hif-1αA andHif-2αA in the heart was up-regulated compared to normoxia control. Conclusions The Hif-α genes are identifiedpositively selected in 13 species, but which species under positively selected is not yet clear and needs further study. Theremay be two different gene expression regulations for the schizothoracine fishes to adapt to moderate hypoxic environment and severe hypoxic environment.