To address the roles of doublesex and mab-3-related transcription factor 1 (Dmrt1), forkhead transcription factor gene 2 (Foxl2), and aromatase in sex differentiation of Southern catfish, the cDNA sequences of these genes were isolated from the gonads. Dmrt1a and Dmrt1b were found to be expressed in the gonads, being higher in the testis. A low expression level of Dmrt1b was also detected in the intestine and kidney of the male. Foxl2 was found to be expressed extensively in the brain (B), pituitary (P), gill and gonads (G), with the highest level in the ovary, indicating the possible involvement of Foxl2 in the B-P-G axis. Cytochrome P450 (Cyp)19b was found to be expressed in the brain, spleen, and gonads, while Cyp19a was only expressed in the gonads and spleen. All-female Southern catfish fry were treated with fadrozole (F), tamoxifen (TAM), and 17beta-estradiol (E2) respectively, from 5 to 25 days after hatching (dah). The expression levels of these genes were measured at 65 dah. In the F-, TAM-, and FTAM-treated groups, Dmrt1a and Dmrt1b were up-regulated in the gonad, whereas Foxl2 and Cyp19a were down-regulated, while the expression of Cyp19b in the gonad remained unchanged. Furthermore, down-regulation of Foxl2 and Cyp19b was also detected in the brain. In the E2-treated group, Dmrt1a and Dmrt1b were down-regulated to an undetectable level in the gonad, whereas Foxl2 and Cyp19b were up-regulated in the brain. Consistent with the observed changes in the expressions of these genes, 56, 70, and 80% sex-reversed male individuals were obtained in the F-, TAM-, and F + TAM-treated groups respectively. These results indicate the significant roles of Dmrt1, Foxl2, and Cyp19 in the sex differentiation of Southern catfish.