Overexpression of enhancer of zeste homologue 2 (EZH2), a key component of polycomb proteins, has been linked to aggressive tumor behavior in a variety of cancers. In vitro, hypoxia-inducible factor 1α (HIF-1α) transcriptionally activates EZH2 and promotes the progression of breast tumor initiating cells. Here, we characterized the clinicopathological effect of EZH2 and HIF-1α in 410 breast cancer patients. We examined EZH2 and HIF-1α expression using immunohistochemistry and western blotting. We found that EZH2 and HIF-1α were highly expressed in 99 (24.1%) and 272 (70.6%) patients, respectively. EZH2 overexpression was associated with lymphatic invasion (P=0.025), HER2 expression (P=0.005) and hypoxia (P<0.001). Overexpression of EZH2 predicted a poor 5-year overall survival (OS, 74.8 vs. 93.4%, P=0.001), disease-free survival (DFS, 72.2 vs. 88.6%, P=0.031), local failure-free survival (LFFS, 95.7 vs. 97.9%, P=0.045) and distant metastasis-free survival (DMFS, 75.4 vs. 90.5%, P=0.039). Multivariate analysis confirmed that EZH2 is an independent prognostic factor for OS, DFS and LFFS. Moreover, a positive correlation was identified between EZH2 and HIF-1α (r=0.299, P<0.001). Importantly, tumors coexpressing HIF-1α and EZH2 had a poorer OS (P=0.007). In conclusion, our study demonstrated that EZH2 is an independent negative prognostic biomarker for breast cancer. Tumors overexpressing HIF-1α and EZH2 are more prone to disease progression.