To identify the relevant CpG sites as molecular markers, for the diagnosis and to distinguish the indolent and aggressive prostate tumors, we have determined the methylation status of 8 genes, including FLNC, EFS, ECRG4, RARB2, PITX2, GSTP1, PDLIM4, and KCNMA1 in 32 nonrecurrent, 32 recurrent primary prostate tumors, and 32 benign prostate tissues using EpiTYPER technology. Specific CpG site hypermethylation of RARB2 and GSTP1 CpG sites were useful for diagnosis of prostate cancer. Furthermore, CpG site hypermethylation of genes FLNC, EFS, ECRG4, PITX2, PDLIM4, and KCNMA1 were associated with prediction of biochemical, local, and systemic recurrence of prostate cancer.