Drosophila melanogaster cuticular pheromones consist of unsaturated hydrocarbons with at least one double bond in position 7: 7 tricosene (T) in males and 7,11 heptacosadiene (HD) in females. However, in many African populations like the Tai strain, females possess low levels of 7,11 HD and high levels of its positional isomer 5,9 HD. We have previously isolated a desaturase gene, desat1, from the Canton-S strain (CS), a 7,11 HD-2-rich morph of D. melanogaster. This desaturase is located in 87C, a locus that has been involved in the difference between 7,11 HD and 5,9 HD morphs. Therefore, we have searched for different desaturase isoforms in both strains. We first cloned desat1 in the Tai strain and report here functional expression of desat1 in CS and Tai. In both strains, the Desat1 enzymes have the same Delta9 specificity and preferentially use palmitate as a substrate, leading to the synthesis of omega7 fatty acids. Also found was a desaturase sequence, named desat2, with a homologous catalytic domain and a markedly different N-terminal domain compared with desat1. In CS genome, it lies 3.8 kb upstream of desat1 and is not transcribed in either sex. In the Tai strain, it is expressed only in females and acts preferentially on myristate, leading to the synthesis of omega5 fatty acids. We suggest, therefore, that desat2 might play a control role in the biosynthesis of 5,9 HD hydrocarbons in Tai females and could explain the dienic hydrocarbon polymorphism in D. melanogaster.