Hypoxia promotes tumor progression through multiple mechanisms including modifying angiogenesis, metabolism switch and invasion. Hypoxia inducible factors (HIFs), particularly HIF1α and HIF2α, are key mediators in cancer hypoxia response and high expression levels of HIFs correlate with a poor prognosis in various tumor types. Cancer stem cells (CSCs), also known as cancer initiating cells or tumor propagation cells, are neoplastic cells that could self-renewal, differentiate as well as initiate tumor growth in vivo. Cancer stem cells are believed to be the key drivers in tumor growth and therapy resistance. Hypoxia has been shown to help maintain multiple normal stem cell population but its roles in cancer stem cells were largely unknown. Our group and other researchers recently identified that hypoxia is also a critical microenvironmental factor in regulating cancer stem cells' self-renewal, partially by enhancing the activity of stem cell factors like Oct4, c-Myc and Nanog. The effects of hypoxia on cancer stem cells seem to be primarily mediated by HIFs, particularly HIF2α. HIF2α is highly expressed in cancer stem cells in gliomas and neuroblastomas and loss of HIF2α leads to significant decrease in cancer stem cell proliferation and self-renewal. These findings illustrated a new mechanism through which oxygen tension and microenvironment influences cancer development. Targeting hypoxia niches may therefore improve therapy efficacy by eliminating cancer stem cell population.