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Hunter harvest data suggest that feral hog (Sus scrofa) populations in western Louisiana are increasing, and population control in this region is complicated by the mixing of feral and domestic free-ranged hogs. Aggressive management may be warranted as feral and domestic hogs appear to be having unexpected effects on their ecosystem. We present the results of 3 recent investigations of genetic source-tracking to link waterborne bacteria with bacteria from feral hogs. We integrate our most recent findings with data regarding: (1) water quality in a watershed without hog management and (2) aquatic biota of the same watershed. Hog activity substantially increased waterborne bacteria, which often exceeded state and federal surface water guidelines. Aquatic biota, specifically freshwater mussels and aquatic insects of the collector and scraper feeding guilds, declined in stream reaches with hog activity. Finally, PCR (polymerase chain reaction)-based DNA source-tracking revealed a >95% similarity between coliform bacteria isolated from water and bacteria isolated from a feral hog harvested within the sample watershed. Further, when the isolated bacteria from the feral hog and water were compared with 900 other bacteria samples from a variety of domestic animals and wildlife, the bacteria isolated from the feral hog and water differed from the 900 other samples. These data suggest that the increasingly abundant hogs of western Louisiana are not only causing detriment to terrestrial flora and fauna, but are negatively impacting native freshwater mussels (Bivalvia unionacea) and insects, as indicated by genetic source-tracking methods.