Mobile DNA sequences - transposable elements (TEs) that amplify and move within genomes represent a high proportion of the DNA in most eukaryotes. The present study aimed to define TE nature, structure and abundance in two contrasting groups of diploid and polyploids crop genera, Brassica (dicotyledon) and Musa (monocotyledon). Rather than starting with known TE sequences, a sequence-data driven approach was used, comparing homologous and homoeologous BAC pairs. Over ~100 kb regions, any stretch of sequence was characterized that was inserted or deleted in the evolutionary time since divergence of the two BAC genomic sequences. Almost all the sequences were indeed TEs, representatives of existing and a few novel superfamilies. Polymorphisms due to activity were measured by PCR with flanking primers in 40 (Brassica) or 96 (Musa) accessions, and some families were localized on chromosomes by fluorescent in situ hybridization. Autonomous and non-autonomous TEs were found; class I retrotransposons like Copia and Gypsy (LTR) predominated in both genera, while SINEs and LINEs (Non-LTR) were abundant in Brassica genomes. Large retrotransposon derivatives (LARDs) were in both genera, with a very few terminal-repeat in miniature (TRIM) elements. Class II DNA transposons included CACTA, hAT, Harbinger, Mariner and Mutator like MITEs in Brassica, while CACTA and Mutator were uncommon in Musa. Among miniature inverted-repeat transposable elements (MITEs), Stowaway, Tourist, and Mutator-like MITEs were abundant with several novel families identified and characterized. In diploid and allopolyploid Brassica species, A- or C-genome specific elements were found while others were more active. PCR enabled accession identification and phylogenetic reconstruction in Brassica and Musa. As well as known element families, few novel types of TEs were identified, including several variable, short elements with characteristic structural features. The analysis provides insight into the nature and diversity of TEs as an important genomic component; results are useful for genome annotation and understanding evolution and variation within these crops and the associated pool of wild germplasm.