Prostate cancer (PCa) proliferation is dictated by androgen receptor (AR) signaling, which regulates gene expression through cis-regulatory regions including proximal and distal enhancers. The repertoire of AR interactions at enhancers is dependent on tissue and cellular contexts and thus shape a spectrum of phenotypes through such epigenetic heterogeneity. Moreover, PCa is a multifocal disease and displays a high degree of intra- and inter-tumor heterogeneity, adding to the phenotypic complexity. It is increasingly becoming clear that PCa may be considered an epigenetic disease caused by various molecular causes with profound consequences and clinical implications which are underpinned by enhancer interaction heterogeneity.In this review, we provide a detailed overview of molecular interactors that affect prostate cancer epigenetic heterogeneity, such as coding and non-coding somatic variants, large scale structural variations, pioneer factor binding at enhancers and various contexts that influence enhancer engagement heterogeneity in PCa development and progression. Finally, we explore how the vast heterogeneity in epigenetic profiles identified in recent omics studies results in distinct genomic subtypes which predict disease progression and thus offer opportunities in biomarker discovery and further personalizing cancer treatment. As such, heterogeneous enhancer interactions take center stage in elucidating mechanisms of prostate cancer progression, patient prognostication, therapy discovery and overcoming acquired treatment resistance.