The genes janus (jan) A and B, and serendipity (sry) beta and delta are two pairs of duplicated genes that are adjacent to each other on the third chromosome of Drosophila melanogaster. The jan A and sry beta genes are expressed throughout development in both males and females. They are transcribed in opposite orientations from start sites separated by only 173 bp of DNA. We report here the complete sequence of the jan A and B genes in Drosophila pseudoobscura, a species distantly related to D. melanogaster in which the overall organization of the sry beta, jan A and jan B genes is identical to that in D. melanogaster. Sequence comparison of the jan A-sry beta intergenic region and 5'-transcribed domain of each gene between D. melanogaster and D. pseudoobscura reveals short stretches of conserved sequences that may correspond to cis-acting regulator elements. In order to test the possibility that some cis-acting regulatory sequences are shared by the two genes, we carried out a deletion analysis of the jan A/sry beta intergenic region in D. melanogaster using transgenic lacZ fusion genes. Our results show that sry beta cis-acting sequences are located in the (-117; +137) 5'-region of the gene and that jan A cis-regulatory sequences are included in the (-56; +151) 5'-domain of this gene. Together these data indicate that in spite of the physical proximity of the jan A and sry beta genes, their transcription is regulated by separate cis-acting sequences.