The Phaseolus genus is the most important grouping of grain legumes for human consumption, representing 75% of all human consumed legumes. With the prevalence of wild and domesticated species, Phaseolus makes a great tool to exploit for comparing evolution over approximately 6 million years, including the impact of humans on speciation. A highly-repetitive, 130 kb bacterial artificial chromosome (BAC) from P. vulgaris was fully sequenced and annotated, which showed that this relatively small piece of DNA represented approximately 30% of the entire genome. The entire BAC and subclones from the BAC were hybridized to genomic DNA blots and chromosome spreads via fluorescence in situ hybridization (FISH) unexpectedly showed that several repetitive elements (mostly retrotransposons) are conserved across the genus. These results show that the typically unique retrotransposons can be conserved during evolution and change the previously understood roles of retrotransposons in evolution.