Objective Histone deacetylase (HDAC) promoted growth and metastasis of prostate cancer cell and it’s action mechanism, however, remain unclear. The aim of present study is investigate the suppression and action mechanism of malignant phenotype by downregulating expression of histone deacetylase (HDAC1 and HDAC2) in prostate cancer cell. Methods Prostate cancer cell lines, LNCaP and DU145 cells were transfected with siHDAC using liposome 2000 or treated with MHY219, named as LNCaP-siHDAC, DU145-siHDAC cells negative control LNCaP-NC small interfering RNA (siRNA), DU145-NCsiRNA cells, and the expressions of HDAC1, HDAC2, HDAC3, matrix metalloproteinase (MMP)-1, MMP-2, MMP-9 and TIMP-1 protein were determined by Western blotting and the levels of MMP-1, MMP-2, MMP-9 and TIMP-1 mRNA were detected using Real time RT-PCR. Cell viability, clone formation ability and metastasis were monitored using MTT, clone formation assay and Transwell respectively in LNCaP and DU145 cells. Results The relative expression levels of HDAC1 and HDAC2 protein was respectively 0.22±0.01, 0.25±0.02 in LNCaP-siHDAC cell and 0.15±0.01, 0.30±0.03 in DU145-siHDAC cell, and significantly lower than LNCaP-NCsiRNA (1.00±0.05, FLNCaP=289.440, P=0.008) and DU145--NCsiRNA (1.00±0.03, FDU145=336.125, P=0.002). The relative expression levels of HDAC1 and HDAC2 protein was respectively 0.53±0.04, 0.60±0.02 in LNCaP cell and 0.58±0.04, 0.66±0.05 in DU145 cell treated with MHY219, and significantly lower than Untreated group (FLNCaP=147.158, P=0.022; FDU145=134.573, P=0.035). The results from the MTT indicated that cell viability was respectively (40.38±4.16)% in LNCaP-siHDAC cell and (21.42±5.26)% in DU145-siHDAC cell with statistical differences compared with LNCaP-NCsiRNA cell [(98.47±6.70)%, FLNCaP=125.627, P=0.004] and DU145-NCsiRNA cell [(99.15±7.00)%, FDU145=137.560, P=0.000]. The cell viability was respectively (61.75±7.12)% and (45.00±5.53)% in LNCaP cell and DU145 cell treated with MHY219, and with statistical differences compared with Untreated group LNCaP [(99.34±7.12)%, FLNCaP=88.392, P=0.032] and DU145 [(98.58±8.05)%, FDU145=103.10, P=0.017]. The results from clone formation assay shown that clone formation rate was respectively (26.37±3.50)% in LNCaP-siHDAC cell and (19.48±2.33)% in DU145-siHDAC cell, and with statistical differences compared with LNCaP-NCsiRNA cell [(97.20±7.88)%, FLNCaP=287.653, P=0.000] and DU145-NCsiRNA cell [(99.23±9.52)%, FDU145=315.042, P=0.000]. The clone formation rate was respectively (43.88±4.12)% and (438.05±6.11)% in LNCaP cell and DU145 cell treated with MHY219, and with statistical differences compared with Untreated group LNCaP [(100.00±5.24)%, FLNCaP=203.540, P=0.018] and DU145 [(97.70±8.74)%, FDU145=264.110, P=0.010]. Transwell results indicated that the cell number of metastasis was respectively (102.5±7.5) in LNCaP-siHDAC cell and (95.2±4.7) in DU145-siHDAC cell and significantly lower LNCaP-NCsiRNA cell (236.8±12.7, FLNCaP=316.047, P=0.00) and DU145-NCsiRNA cell (278.5±18.6, FDU145=357.052, P=0.000). Western blotting and Real time RT-PCR results shown that downegulated HDAC1 or (and) HDAC2 expression notable suppressed the expression of MMP-1and MMP-2 in protein and mRNA levels, but TIMP-1 expression was significantly enhanced in LNCaP and DU145 cells. Conclusion The suppression of malignant phenotype by downregulating expression of HDAC1 and HDAC2 in prostate cancer cell. Downregulated HDAC expression can inhibited malignant phenotype and it’s action mechanism was achieved at least partly by regulating expression of MMP-1, MMP-2 and TIMP-1 expression in LNCaP and DU145 cells. Key words: Prostate cancer; Histone deacetylase; Matrix metalloproteinase; Malignant phenotype; Action mechanism