MicroRNA-429(miR-429) plays an important role in mesenchymal stem cells. Hypoxia-inducible factor 1 (HIF-1) is a nuclear transcription factor that regulates the proliferation, apoptosis and tolerance to hypoxia of mesenchymal stem cells. HIF-1 is also a target gene of miR-429. We investigated whether miR-429 plays a role in hypoxia tolerance with HIF-1 in human amniotic mesenchymal stem cells (hAMSCs). The expression of miR-429 was increased by hypoxia in hAMSCs. miR-429 expression resulted in decreased HIF-1 protein level, but little effect on HIF-1 mRNA. While overexpression of HIF-1 increased the survival rate and exhibited anti-apoptosis effects in hAMSCs under hypoxia, co-expression of miR-429 reduced survival and increased apoptosis. However, miR-429 silencing with HIF-1 overexpression stimulated cell survival and reduced apoptosis. Co-expression of HIF-1 and miR-429 reduced VEGF and Bcl-2 proteins and increased Bax and C-Caspase-3 levels in hAMSCs under hypoxia compared with cells expressing only HIF-1; cells with HIF-1 overexpression and miR-429 silencing showed the opposite effects. These results indicate that HIF-1 and angomiR-429 reciprocally antagonized each other, while HIF-1 and antagomiR-429 interacted with each other to regulate survival and apoptosis in hAMSCs under hypoxia. miR-429 increased VEGF and Bcl-2 protein levels and decreased Bax and cleaved Caspase-3 protein levels by promoting the synthesis of HIF-1. These results indicate that miR-429 negatively regulates the survival and anti-apoptosis ability of hAMSCs by mediating HIF-1 expression and improves the ability of hAMSCs to tolerate hypoxia.