The presence of piscivorous fish has a significant effect on the structure of fish assemblages. Exotic, piscivorous largemouth bass (Micropterus salmoides) have been introduced to a number of Japanese farm ponds that were originally characterized by a high level of biodiversity. We evaluated the effects of exotic bass on the structure of the fish assemblage following their introduction into the farm ponds. We collected fish and measured environmental conditions in 14 ponds of northeastern Japan. The species richness of pond-dwelling fish assemblages was negatively correlated with the relative abundance of exotic bass. In addition, the relative abundance of lentic cyprinid species (e.g., Rhodeus ocellatus ocellatus, Pseudorasbora parva and Carassius sp.) was negatively correlated with the relative abundance of exotic bass. The abundance of these species was also influenced by environmental factors, including transparency and/or coverage of aquatic vegetation, likely related to their influence on the predatory efficiency of exotic bass. Our results suggest that the structure of fish assemblages in farm ponds with exotic piscivorous fish was influenced by both biotic (i.e., predation) and abiotic factors and that some environmental factors mediate the effects of exotic bass on fish species richness and composition.