Key message We provided a chromosome-length assembly of B. nigra and show the comprehensive chromosome-scale variations among Brassica genomes. Chromosome-level assembly of the Brassica species, which include many important crops, is essential for the agricultural and evolutionary studies. While the present B. nigra chromosomes was connected with genetic map of B. juncea , hindering the comparative analysis of the B chromosomes. Here we present a chromosome-length B. nigra assembly constructed with Hi-C connections and its variations on chromosome level compared with other Brassica species. We produced an assembly of 484 Mb annotated with 51,829 genes, of which 393 Mb were anchored onto 8 chromosomes, taking 81.26% of the assembly. Comparison of the B chromosomes shows high concordance of the two B. nigra assemblies and reveals comprehensive variations of the B chromosomes after polyploidization and gene loss in syntenic regions. Chromosome blocks with variations have lower gene density and higher TE content. Furthermore, we compared the chromosomes of the three major Brassica diploids, which showed that most of the variations between B and A/C had completed before A/C divergence and there are more variations on C chromosomes after their divergence. In summary, our work presents a chromosome-length assembly of B. nigra and comprehensive comparative analysis of the Brassica chromosomes, which provides a useful reference for other studies and comprehensive information of Brassica chromosome evolution.