Pteronotus is a Neotropical genus of mormoopid bats known to form large colonies in caves. Cave selection by Pteronotus is not random, and maternity roosts are characterized by the presence of a hot chamber where females give birth and raise their young. Such bat caves are unique from ecological and conservationist perspectives. Previous studies on bat caves in the drylands of Brazilian northeastern region - some holding up to 150,000 bats - have shown that P. gymnonotus presented no population structuring, with no correlation between geographical and genetic distance, and that bat caves up to 700 km apart form a very dynamic roost network used by that species. P. personatus is a smaller relative found in sympatry with P. gymnonotus. Both species frequently share the same roosts and are exposed to similar environmental conditions when foraging; therefore, they are good candidates for a comparison of their population genetic structuring. Using ddRADseq methodology, 55,836 SNPs from 72 P. personatus (21 females and 51 males) and 37,037 SNPs from 177 P. gymnonotus (93 females and 84 males) were analyzed. We observed that both species presented no strong signs of population genetic structure in the drylands of northeastern Brazil, and geographic distance is not the main factor shaping their genetic connectivity. Furthermore, our results suggest that the two Pteronotus species studied are characterized by very dynamic roost use, meaning that individuals frequently switch among caves within a landscape rather than relying on a single permanent roost. Thus, indicating that conservation initiatives should not rely solely on single-site protection but rather adopt a landscape-scale perspective.