In this study, the cDNA sequences of HSP70 and HSP90 were isolated from the special chondr-ganoid scale, Amur sturgeon, for the first time. Homology analysis indicated that amino acid sequences of HSP70 and HSP90 shared high identity with other species (82.68-99.07 and 90.19-98.07%, respectively). The tissue expression analysis showed that the asHSP70 and asHSP90 mRNA were ubiquitously expressed in all the examined tissues under unstressed condition. The expression pattern of HSP70 and HSP90 under chronic (crowding) and acute (hypoxia) stress was examined by q-PCR in liver, spleen and kidney. Results showed that stocking density could significantly influence the expression of HSP70 at day 20 and/or day 40. In contrast to stocking density, levels of HSP70 transcripts indicated a remarkable increase in all examined tissues after hypoxia stress. HSP90 levels in liver and spleen increased significantly in high stocking density. By comparison, significant increase of asHSP90 in kidney was only found in high stocking density at day 40. Similar to HSP70, the levels of HSP90 transcripts showed significant increases after hypoxia stress except the transcript of liver in H2 group 6 h after hypoxia. The assessment of asHSP70 and asHSP90 mRNA levels under crowding and hypoxia stresses indicated that asHSP70 and asHSP90 gene might be good indicators of stressful situations for Amur sturgeon. Taking serum globulin and electrolytes account, we suggest that crowding and hypoxia stress can result in considerable stress for Amur sturgeon.