B-cell CLL/lymphoma 9 protein (BCL-9), a multi-functional co-factor in Wnt signaling, induced carcinogenesis as well as promoting tumor progression, metastasis and chemo-resistance in colorectal cancer (CRC). However, the mechanisms for increased BCL-9 expression in CRC were not well understood. Here, we report that hypoxia, a hallmark of solid tumors, induced BCL-9 mRNA expression in human CRC cells. Analysis of BCL-9 promoter revealed two functional hypoxia-responsive elements (HRE-B and HRE-C) that can be specifically bound with and be transactivated by hypoxia inducible factors (HIF) 1 alpha but not HIF-2 alpha. Consistently, ectopic expression of HIF-1 alpha but not HIF-2 alpha transcriptionally induced BCL-9 expression levels in cells. Knockdown of endogenous HIF-1 alpha but not HIF-2 alpha by siRNA largely abolished the induction of HIF by hypoxia. Furthermore, there was a strong association of HIF-1a alpha expression with BCL-9 expression in human CRC specimens. In summary, results from this study demonstrated that hypoxia induced BCL-9 expression in human CRC cells mainly through HIF-1 alpha, which could be an important underlying mechanism for increased BCL-9 expression in CRC.