A putative stock of largemouth bass Micropterus salmoides, characterized by small adult size and large condition factors, exists in the Mobile Bay or delta region of the Alabama River system. High salinity often occurs in this area of the river. Populations from the delta (mesosaline), Tombigbee River (fresh water), and Alabama River (fresh water), all in the Alabama River system, were electrophoretically compared to one another and to populations from other watersheds in Alabama. Largemouth bass from the Alabama River system were genetically distinct from those of other watersheds. Minimal allele-frequency differences were observed among delta, Tombigbee, and Alabama populations. Observed allele frequencies of delta and Tombigbee fish were more similar to each other than to those of Alabama River fish. Mean heterozygosity was 0.027, 0.019, and 0.004 for delta, Tombigbee, and Alabama River populations, respectively. Delta largemouth bass had a different (P = 0.05) allele frequency from Tombigbee and Alabama fish at the esterase-B locus. The smaller size and greater condition of delta largemouth bass relative to fish further upstream are probably due to environmental factors, because observed genetic differences were minimal. However, delta and upstream fish need to be grown in the same environment to determine the relative influences of environment and genetics on the body conformation of delta largemouth bass.