Prostate cancer presents a high degree of heterogeneity in pathology, clinical biology and molecular spectrum. Some men suffer from indolent prostate cancer that can be followed safely, while others have aggressive, lethal prostate cancer. In the past decade, researchers have begun to unravel the genomic heterogeneity that contributes to these different clinical phenotypes. The emergence of different molecular subtypes has the potential to translate this disease from an unknown and highly variable heterogeneous disease into a collection of molecular subtypes. The uniqueness of these subclasses has been used to predict clinical outcomes, to design novel biomarkers for the diagnosis of prostate cancer and to develop new therapeutic agents. In this paper, we review some of the molecular subtypes of prostate cancer, with an aim to provide clues to future development of strategies for treating prostate cancer.