Nsa cytoplasmic male sterility (CMS) is a novel Brassica napus male sterility system derived from Sinapis arvensis cytoplasm. Nsa CMS results in defective pollen production due to S. arvensis mitochondrial gene failure/incompatibility in the anthers, requiring nuclear genes to restore fertility. From ultramicroscopic observation of anther sections, we concluded that the induction of sterility begins at the pollen (microspore) mother cell stage. Most pollen mother cells do not undergo the first meiotic division and dissociate before the tetrad stage. At the tetrad stage, abortion was observed for all uninucleate pollen. Dysfunction of mitchondrial gene(s) leads to cell vacuolization in the anther tapetum and middle layer cells. Early programmed cell death (PCD) of the tapetum and anther middle layer cells is the main reason for pollen mother cell abortion. Due to this early pollen abortion, the sterility of Nsa CMS is stable and complete. Southern blotting of DNA from the Nsa male-sterile line, its maintainer and restorer lines, as well as the two parental lines (B. napus cv. Zhongshuang 4 and S. arvensis var. Yeyou 18) involved in the somatic hybridization, suggested that the cytoplasm of the Nsa CMS line was from S. arvensis and that of the restorer line was a rearrangement of both parental lines. Nsa CMS shows great potential for hybrid seed production in rapeseed. Our results provide clues to identify novel male-sterility (S) and restorer (R) genes as well as elucidate the mechanism underlying interactions between the S and R genes.