The objective of the present study was to identify prostate cancer stem cells and determine the effects of modulating specific miRNAs on prostate CSC proliferation and apoptosis. We applied flow cytometry sorting of side population cells to cultures of prostate cancer cell lines (TSU, DU145, PC-3 and LNCaP). The proportion of SP cells in the TSU line was 1.60 +/- 0.40% (mean SD), while that of the DU145, PC-3 and LNCaP lines was 0.60 +/- 0.05, 0.80 +/- 0.05 and 0.60 +/- 0.20%, respectively. Because the proportion of SP cells derived from TSU cells is greater, these cells were selected to sort side population cells and non-side population cells. The stem-like properties of SP cells had been identified by in vivo and in vitro experiments, and the related study was published. RNA was extracted from the SP cells and non-SP cells and analyzed using miRNA microarray technology. Fifty-three miRNAs with significant differences in their expression were detected in total. Furthermore, 20 of these miRNAs were validated by qPCR. We found that hsa-miR-149 expression in SP cells and non-SP cells was significantly different; hsa-miR-149 was significantly upregulated in SP cells. By constructing a vector for lentiviral infection, we found that the downregulation of hsa-miR-149 leads to a reduction in proliferation, an increase in apoptosis, and a significant reduction in the colony formation potential, thus, inhibiting tumor growth in vivo of SP cells from the TSU cell line. The present study will provide new avenues toward understanding the function of prostate cancer stem cells (PCSCs) in tumorigenicity and metastasis.