We examined aspects of the ecology of an isolated population of critically imperiled Enneacanthus chaetodon (Blackbanded Sunfish) in the only known extant locality in Maryland and made comparisons with an abundant and widespread sympatric congener, E. gloriosus (Bluespotted Sunfish). For Blackbanded Sunfish, we found population sizes were small, with abundance and age structure fluctuating throughout the course of the 9 years of observation, very low genetic diversity, and elevated levels of inbreeding. Habitat associations revealed a strong association of Blackbanded Sunfish with aquatic vegetation. We estimated a lifespan of 3–4 years for Blackbanded Sunfish, based on modal decomposition of length–frequency histograms. Bluespotted Sunfish exhibited much more stable population dynamics, larger population size, and a longer lifespan of 4–5 years. Our results indicate isolated Blackbanded Sunfish populations exhibit a clear susceptibility to environmental stochasticity and are unlikely to persist without intervention. More broadly, our results suggest that the long-term persistence of this species in much of its range is likely dependent on increasing connectivity between existing populations, (re)establishing populations in viable localities, maintaining suitable habitat, and reducing pressures from introduced centrarchids.