Adipose-derived mesenchymal stem cells (ADMSCs) and nucleus pulposus-derived mesenchymal stem cells (NPMSCs) are two cell candidates for cell-based therapies for intervertebral disc (IVD) regeneration. However, little work has been done to determine the influence of hypoxia in the IVD on the biological behaviors of ADMSCs and NPMSCs. This study aimed to investigate the viability, proliferation and differentiation of rat ADMSCs and NPMSCs in the hypoxic environment of IVD in vitro. ADMSCs and NPMSCs isolated from 6 SD rats were cultured under normoxia (20% O2) and hypoxia (2% O2) mimicking the standard condition and hypoxic environment of the IVD for 14 days. Cell viability was determined by the annexin-V-FITC/propidium iodide double-staining assay and cell proliferation was measured by MTT assay. The expression of hypoxia-inducible factor-1α, glucose transporter (GLUT)-1, GLUT-3 and vascular endothelial growth factor-A at the mRNA level was examined by RT-PCR. In cells cultured in three-dimensional micromass and differentiation medium, aggrecan, collagen-II and Sox-9 expression at mRNA and protein levels were examined by RT-PCR and Western blot. Hypoxia inhibited the viability and proliferation of both ADMSCs and NPMSCs, but promoted the chondrocytic differentiation of ADMSCs and NPMSCs. Compared to ADMSCs, NPMSCs showed greater viability, proliferation and chondrocytic differentiation under hypoxia. In conclusion, hypoxia in the IVD had a significant impact on the viability, proliferation and chondrocytic differentiation of ADMSCs and NPMSCs. NPMSCs exhibited more potent biological activity than ADMSCs in the hypoxic environment of the IVD and may represent another candidate for cell-based therapy for IVD regeneration.