Population declines of amphibians and reptiles throughout the world have led to the initiation of projects to monitor their status and trends. Historical collections give an indication of which species occurred in an area at one time, although the ambiguity surrounding locations and environmental conditions associated with collection decreases the value of this information source. Resampling using the same general protocols can give valuable insights to changes in community structure. However, this is only feasible when sampling methodology and exact site locations are known. From 2002–2005 we resampled 12 sites in St. Marks National Wildlife Refuge in Florida's panhandle, an area in which intensive herpetological surveys were conducted in 1977–1979. We documented a general decrease in species richness among the diversely managed sites, changes in dominant species and diversity and an increasing trend toward homogeneity of the herpetofaunal community among habitats. Changes were attributed to four causes: 28-y of forest community succession, changes in management practices, non-detection of species due to variation in sampling conditions and a decrease in occupancy by four amphibians and three reptiles. The use of population and habitat-related indexes helped define possible influences on community change and can be used to target species for monitoring. Declines of these seven species are of concern, especially considering the protected status of the refuge and its increasing isolation as surrounding landscapes are converted to urbanized settings.