Raptor roosts, as accumulations of expelled pellets and nest material, serve as archives of past and present small mammal communities and could therefore be used to track invasive species population dynamics over time. We tested the utility of this resource and added new information towards reconstructing the phylogeographic history of a globally invasive species in the Caribbean, the black rat (Rattus rattus) using skeletal remains from a raptor roost deposit located within a limestone cave in the Dominican Republic (Tres Bocas). As a tropical environment, Caribbean bones are typically poorly preserved. Thus, we applied next generation sequencing techniques commonly used in ancient DNA (aDNA) studies to reconstruct a nearly complete R. rattus mitochondrial genome from such a deposit. Phylogenetic analyses indicated a putative source R. rattus haplotype clade A-I for the Tres Bocas sample, which originates from southern India. Our results serve as a proof-of-concept that aDNA techniques could be used to unlock past histories of small mammal populations from raptor roost deposits in tropical island settings, where invasive mammals are among the greatest conservation concerns.