Background: Short interspersed elements (SINEs) have a powerful influence on genome evolution and can be useful markers for phylogenetic inference and population genetic analyses. In this study, we examined survey sequence and whole genome data to determine the evolutionary dynamics of Ves SINEs in the genomes of 11 bats, nine from Vespertilionidae. Results: We identified 41 subfamilies of Ves and linked several to specific lineages. We also revealed substantial differences among lineages including the observation that Ves accumulation and Ves subfamily diversity is significantly higher in vesper as opposed to non-vesper bats. This is especially interesting when one considers the increased transposable element diversity of vesper bats in general. Conclusions: Our data suggest that survey sequencing and genome mining are valuable tools to investigate SINE evolution among related lineages and can provide substantial information about the ability of SINEs to proliferate in diverse genomes. This method would also be a useful first step in determining which subfamilies would be the best to target when developing SINEs as markers for phylogenetic and population genetic analyses.