The ovarian hormone progesterone regulates normal female reproductive physiology and is essential for normal development and function in the breast. However, exposure to progesterone analogues in hormone replacement therapy confers an increased risk of breast cancer. Progesterone effects are mediated by its nuclear receptor (PR), expressed as two isoforms, PRA and PRB, which play distinct functional roles. Hormone binding elicits receptor dimerization and binding to DNA, resulting in transcriptional regulation. PRA and PRB are equivalently expressed in normal epithelial cells; however over-expression of one isoform, is common in breast cancer, suggesting that altered isoform expression may underlie an aberrant transcriptional response to progestins in malignancy. Using genome-wide chromatin immunoprecipitation sequencing (ChIP-seq), we previously demonstrated that PR genomic interaction is cell type-specific and that transcriptional partners influence PR binding. Analysis of PR binding site sequences revealed considerable divergence from a conserved consensus progesterone response element (PRE). Moreover, PRE conservation did not predict binding strength or transcriptional outcome. Further analysis revealed that the presence of motifs for transcriptional partners acting as pioneer factors for PR allowed the PRE to diverge more from the consensus than in sites lacking binding partner motifs, suggesting that transcriptional partner availability regulates cell type-specific response to progesterone. Characterisation of individual PRA and PRB cistromes in breast cells revealed that while there was considerable overlap between the binding sites for PRA and PRB, many sites were unique to just one isoform. A similar consensus PRE was identified with each isoform, however motifs for pioneer factor AP-1 were significantly more strongly enriched in PRA binding sites than in sites exclusive to PRB. This differential enrichment of cofactor motifs in PRA and PRB binding sites suggests that the level of AP-1 expression in breast cells may influence transcriptional response, particularly in malignancy when PRA often becomes the predominant species.