Enneacanthus chaetodon, the blackbanded sunfish, has become increasingly rare throughout its distribution in the Eastern United States. In Virginia, E. chaetodon maintains an endangered status and individuals persist in six populations. Mitochondrial DNA (mtDNA) and microsatellite data were assessed to determine the genetic characters and gene diversity of the Virginia populations. The results of these analyses were then compared to five additional populations; four from New Jersey and one from North Carolina that were known to have relatively good fitness and were not impacted severely by habitat alteration. The results of this study are relevant to selection of proper management techniques and strategies for this species. Mitochondrial DNA analyses detected no variation in the Virginia populations but significant (P F > 0.2) of inbreeding. The New Jersey and North Carolina populations demonstrated lower amounts of inbreeding than populations in Virginia. New Jersey displayed a significant (P < 0.05) amount of subdivision among populations compared to Virginia. Hypothesis testing supported the contention that the regions are significantly different from one another and that Virginia populations may have gone through one or more population bottlenecks in the past, explaining the low levels of diversity observed and significantly high inbreeding coefficients. Captive breeding programs could be implemented as a management measure to increase population numbers and restore fish into areas where they have been known to inhabit in the recent past. From a proper management perspective, habitat protection and maintenance are more important than supplementation to population survival. Success of either approach with Virginia populations would provide a useful model for managing small populations of blackbanded sunfish in other regions.This project was supported by a grant from the Virginia Department of Game and Inland Fisheries (VDGIF), grant #ED0817BB.