We quantified changes of H3K9me1 or H3K9me2 marks, the two substrates of KDM3A, and mapped AR-binding in the CWR22Rv1 prostate cancer cell line in combination with knockdown of KDM3A. Alteration of H3K9 methylation marks mapped to genomic locations coinciding with AR binding pinpoints target genes and oncogenic pathways cooperatively regulated by KDM3A and AR. Here, KDM3A is linked to prostate carcinoma.