Erythropoietin (EPO) is a glycoprotein hormone that plays a potential role in hypoxic adaptation in animals. In the present study, the encoding sequences of Epo and Epor genes were cloned in Gymncypris eckloni by RT-PCR method. The coding region of Epo and Epor were 552 bp and 1 590 bp, which encoded 183 and 529 amino acid residues respectively (Fig. 1 and 2). The high homology of EPO and EPOR protein of G. eckloni with other cyprinid fishes indicated that the two proteins were evolutionary conserved (Table 2). Molecular evolution analysis suggested that Epo and Epor genes of G. eckloni did not undergo positive selection (Table 3). Under severe (the dissolved oxygen was 0.3 ± 0.1 mg/L) and moderate hypoxic (the dissolved oxygen was 3.0 ± 0.1 mg/L) conditions, the Epo mRNA levels in key tissues such as brain and red muscle were increased significantly (Fig. 4 and 5), implying its potential roles in movement, neuroprotection and neurotrophy, which may be a regulatory mechanism of fish to hypoxic adaptation.