Bactrocera fruit flies are ranked among the most destructive pests of the worldwide fruit and vegetable trades. Coding regions of two oligomerization domains within doublesex (dsx) genes were determined in Bactrocera dorsalis (oriental fruit fly) and B. correcta (guava fruit fly). Resulting sequences revealed a high degree of similarity at both nucleotide and putative amino acid levels in the genus Bactrocera. Conservation of the DNA-binding DM motif and several known molecular features within the domains suggest a presence of strong purifying selection on the DSX proteins. Topology of the phylogenetic gene trees and deduced amino acid substitution patterns suggest that the coding region sequences of the two domains are diversified in concert parallel with the species differentiation.