Changes in androgen signaling during prostate carcinogenesis are associated with both inhibition of cellular differentiation and promotion of malignant phenotypes. The androgen receptor (AR)-binding transcription factor (TF) RUNX2 has been linked to prostate cancer (PCa) progression but the underlying mechanisms have not been fully defined. In this study, we investigated the genome-wide influence of RUNX2 on androgen-induced gene expression and AR DNA binding in PCa cells. RUNX2 inhibited the androgen response partly by promoting the dissociation of AR from its target genes such as the tumor suppressor NKX3-1. However, AR activity persists in the presence of RUNX2 at other AR target genes, some of which are co-operatively stimulated by androgen and RUNX2 signaling. These genes are associated with putative enhancers co-occupied by AR and RUNX2. One such gene, the invasion-promoting Snail family TF SNAI2, was co-activated by AR and RUNX2. Indeed, these two TFs together, but neither alone stimulated PCa cell invasiveness, which could be abolished by SNAI2 silencing. In support of our results, an immunohistochemical analysis of SNAI2 in archived primary PCa specimens revealed a correlation with the RUNX2 histoscore; and, simultaneous strong staining for SNAI2, RUNX2 and AR (but not any pair alone) was associated with disease recurrence. Overall, our findings suggest that AR and RUNX2 cooperate to stimulate certain invasion-promoting genes like SNAI2, which might be targeted for individualized PCa therapy.