Transposable elements (TEs) are ubiquitous in eukaryotes. Their ability to move and replicate is largely responsible for genome expansion and rearrangement. Brassica rapa (AA, N=10) and Brassica oleracea (CC, N=9), which diverged about 4 million years ago, recently formed into Brassica napus (AACC, N=19) by natural hybridization. In this study, we identified 4550 and 13345 transposable elements with clear boundaries in the B.rapa and B.oleracea genomes, respectively. These two diploid species did not show significant difference in TE content. Retrotransposons were found to be the major contributors to the repetitive fractions in both species. Phylogenetic analysis revealed that, except for six Copia and five Gypsy ancient lineages previously described, two new lineages BCR (Brassica Copia Retrotransposon) and BGR (Brassica Gypsy Retrotransposon) were defined in this study. In addition, we compared TE contents in defined syntenic regions between the two diploid species, and found that the proportions of TEs are considerably higher in B.oleracea than in B.rapa. This result is in consistent with the observation obtained from phylogenetic analysis. Although these two genomes are composed of similar amount of TE DNA, they exhibited distinct patterns of TE distributions. Further analysis of the physical association of LTR-RTs with centromere satellite repeats identified three putative centromere retrotransposon (CR) families. Two of them (Family190: Brr163, Bor155; Family608: Bor478) appear to have been functionally specified as centromere components before the divergence of the A and C genomes. The third one (i.e., Family805: Brr363) was identified in B.rapa and B.napus, but not seen in B.oleracea, suggesting that this family may be A genome specific.