To study the gene expression change and possible signal pathway during androgen-dependent prostate cancer(ADPC) becoming androgen-independent prostate cancer (AIPC), an LNCaP cell model of AIPC was establishedusing flutamide in combination with androgen-free environment inducement, and differential expression geneswere screened by microarray. Then the biological process, molecular function and KEGG pathway of differentialexpression genes are analyzed by Molecule Annotation System (MAS). By comparison of 12,207 expressiongenes, 347 expression genes were acquired, of which 156 were up-ragulated and 191 down-regulated. Afteranalyzing the biological process and molecule function of differential expression genes, these genes are foundto play crucial roles in cell proliferation, differntiation, cell cycle control, protein metabolism and modificationand other biological process, serve as signal molecules, enzymes, peptide hormones, cytokines, cytoskeletalproteins and adhesion molecules. The analysis of KEGG show that the relevant genes of AIPC transformationparticipate in glutathione metabolism, cell cycle, P53 signal pathway, cytochrome P450 metabolism, Hedgehogsignal pathway, MAPK signal pathway, adipocytokines signal pathway, PPAR signal pathway, TGF-β signalpathway and JAK-STAT signal pathway. In conclusion, during the process of ADPC becoming AIPC, it is notonly one specific gene or pathway, but multiple genes and pathways that change. The findings above lay thefoundation for study of AIPC mechanism and development of AIPC targeting drugs.