The phylogenetic relationships of genera of the family Centrarchidae and its affinities to the Elassomatidae were examined using the mitochondrial DNA sequences of the cytochrome b gene. A total of 32 individuals representing 16 species from nine genera of centrarchids were sequenced. Outgroup were drawn from other perciform families including several families previously proposed to be closely related to the Centrarchidae. Phylogenetic analysis was conducted using the optimality criteria of maximum parsimony with two weighting schemes and using the maximum likelihood method. A priori and a posteriori alternative hypotheses of relationships within the Centrarchidae were investigated using the Shimodaira and Hasegawa Test. The results of all analyses support the monophyly of the Centrarchidae, although the interrelationships of centrarchid genera differed between analyses. Elassoma was never recovered as the sister taxon to the Centrarchidae; however, the sister relationship of these taxa could not be rejected. Additional data are required to unambiguously resolve relationships among centrarchid genera and determine the relationship of the Centrarchidae to other perciforms.