The SWI/SNF-like chromatin remodeling complex of Drosophila, the Brahma complex, contains four subunits (Brahma, BAP155/Moira, SNR1 and BAP60) conserved from yeast to humans. A reconstituted human complex lacking the BAP60 homolog shows full remodeling activity, suggesting that BAP60 is not essential for the core function. We generated Drosophila mutants and found that BAP60 carries a vital function and participates in complex-mediated transcriptional activation and repression. BAP60 binds DNA and shows genetic and physical interactions with the sex-determining transcription factors encoded by sisterless A and scute. The results support the conclusion that BAP60 participates in site-specific recruitment of the Brahma complex in Drosophila.