We introduce an analysis method to demonstrate correlation between biota and the physical habitats that they occupy. Using the same calculations as does Nei's genetic distance index, this method builds independent dissimilarity matrices for both habitat and fauna, which can then be compared in a common statistical framework. An important advantage of this method is that only frequency data are necessary to perform the analysis. We demonstrate the utility of this method using fish community and habitat data from the Eightmile and Pomperaug rivers in Connecticut. In both cases, there is a significant correlation between biota and habitat. Not only is ecological dissimilarity analysis a useful technique for testing community-to-habitat correlation, it is also an excellent tool for communicating this information to the many non-scientists who shape conservation policy.