Chiropteran mandibles from late Pleistocene/Holocene fossil cave localities in Hamilton County were identified in order to examine changes in bat species diversity and population trends over extended periods of time, providing insight into how bats in Southeast Tennessee have responded to major environmental changes over the past 10,000–20,000 years. Generic and species identifications were based on an unpublished key developed by the authors. Measurements of alveolar length (c1–m3) and total length measurements from the symphysis to the condyle were taken for all specimens identified as members of the genus Myotis in an attempt to identify species in this genus. The results of this study failed to confirm those of previous univariate morphological studies, suggesting that multivariate morphometric analyses may be needed to establish a means to differentiate among the species in this genus. Diversity data indicated two patterns of species abundance, with Eptesicus fuscus (Big Brown Bat) dominating some sites and Myotis sp. dominating others. The data suggest, but do not conclusively demonstrate, that a temporal replacement of older Eptesicus faunas by younger, Myotis-dominated faunas has occurred, connected with post-Pleistocene global warming. In addition, a correspondence between human disturbance and bat populations levels was observed. It is very likely that human disturbance has caused bat populations to become extinct in the caves under study, reinforcing the claim of previous researchers that bat population decline is a recent phenomenon that is tightly linked to human disturbance.