"Regulatory evolution," that is, changes in a gene's expression pattern through changes at its regulatory sequence, rather than changes at the coding sequence of the gene or changes of the upstream transcription factors, has been increasingly recognized as a pervasive evolution mechanism. Many somatic sexually dimorphic features of Drosophila melanogaster are the results of gene expression regulated by the doublesex (dsx) gene, which encodes sex-specific transcription factors (DSX F in females and DSX M in males). Rapid changes in such sexually dimorphic features are likely a result of changes at the regulatory sequence of the target genes. We focused on the Flavin-containing monooxygenase-2 (Fmo-2) gene, a likely direct dsx target, to elucidate how sexually dimorphic expression and its evolution are brought about. We found that dsx is deployed to regulate the Fmo-2 transcription both in the midgut and in fat body cells of the spermatheca (a female-specific tissue), through a canonical DSX-binding site in the Fmo-2 regulatory sequence. In the melanogaster group, Fmo-2 transcription in the midgut has evolved rapidly, in contrast to the conserved spermathecal transcription. We identified two cis-regulatory modules (CRM-p and CRM-d) that direct sexually monomorphic or dimorphic Fmo-2 transcription, respectively, in the midguts of these species. Changes of Fmo-2 transcription in the midgut from sexually dimorphic to sexually monomorphic in some species are caused by the loss of CRM-d function, but not the loss of the canonical DSX-binding site. Thus, conferring transcriptional regulation on a CRM level allows the regulation to evolve rapidly in one tissue while evading evolutionary constraints posed by other tissues.sex determination | transcription factors | DNA binding site | evolution H ow sex-specific characteristics are generated during development, what roles they have in the biology of an organism, and how they have evolved are fundamental questions in biology. In Drosophila melanogaster, the molecular mechanisms leading to the sex-specific and temporally and spatially restricted deployment of the transcription factors encoded by the terminal genes in the sex-determination regulatory hierarchy, doublesex (dsx) and fruitless (fru), have been well documented (1-4). In addition, although it has been established that the FRU M and DSX M and DSX F proteins control nearly all aspects of somatic sexual differentiation, including anatomical and behavioral differences, much less is known about the direct target genes through which these transcription factors act (2, 3, 5-11).It has been increasingly recognized that evolutionary significant changes in gene expression are often a result of mutations in the regulatory sequences of genes, rather than in their coding sequences (12). Furthermore, it has been noted that evolutionary changes are most likely in the cis-acting regulatory elements of the downstream targets of transcription factors, rather than in the genes encoding the transcription factors (13,14). This finding...