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Past and ongoing human activities have shaped the geographical ranges and diversity of species. New genomic techniques applied to degraded samples, such as those from natural history collections, can uncover the complex evolutionary consequences of human pressures and generate baselines for interpreting magnitudes of species loss or persistence relevant to conservation. Here we integrate mitogenomic data with historical records from a recently rediscovered Bahamian hutia ( Geocapromys ingrahami ; (FMP Z02816)) specimen at the Fairbanks Museum & Planetarium (Vermont, USA) to determine when and where the specimen was collected and to place it in a phylogenetic context with specimens that both predate (palaeontological) and postdate (archaeological) human arrival in The Bahamas. We determined that this specimen was part of the same population as the named holotype specimen in 1891 on East Plana Cay (EPC). Bahamian hutia populations were widely extirpated following European colonization. Today, EPC hosts the last remaining natural Bahamian hutia population. Mitogenomic data places the focal specimen within the southern Bahamian hutia population, which is now largely restricted to EPC. The results reveal previously undocumented genetic continuity among the EPC population for at least the past 500 years, highlighting how ‘dark’ museum specimens inform new conservation-relevant understandings of diversity.