Polyploidization has been viewed as a highly dynamic process and a major force in the evolution of higher plants, including many important crops. To better understand the genomic evolution of Brassica polyploids, we used the Brassica triangle, including three allopolyploids and three diploids, to study genomic evolution after the formation of polyploids. Based on the inter-simple sequence repeat (ISSR) analysis, the different degree of A, B or C genomic modifications were observed in the three Brassica allopolyploids. In B-contained allopolyploids, B genome always altered less than the other genome (A or C), showing that B genome was relatively conserved in the evolution of Brassica allopolyploids. ISSR data supported that a higher degree of ancestral genomic divergence gave rise to a greater frequency of genomic change of polyploids. The possible mechanisms for the genomic changes and the reason for the relatively conserved B genome were discussed.