Approximately 70%-75% of prostate cancers originate in the peripheral zone (PZ) and 20%-30% in the transition zone (TZ). According to the Prostate Imaging Reporting and Data System (PIRADS), the diagnostic criteria for PZ and TZ is different. To accomplish fully automatic segmentation for the PZ and TZ, we proposed a territory segmentation method for prostate MR images by multi-atlas matching. This novel segmentation method could not only segment the whole prostate (WP) region, but also the PZ and TZ. The proposed method is fully automatic and could achieve high segmentation accuracy.