Color vision is widely used by herbivorous insects to make host location. We have previously demonstrated that the long-wavelength-sensitive (LWS) opsin gene Rhodopsin 6 (Rh6) confers green preference in Bactrocera minax (a specialist) but yellow in B. dorsalis (a generalist). However, the transcriptional regulation underlying Rh6 expression and its association with color preference between these two sister species remains unclear. Here, we cloned the core promoter regions of BmRh6 and BdRh6, and identified the transcription factors (TFs) BmHmx in B. minax and BdPtx1 in B. dorsalis through bioinformatics and transcriptomic analysis. The functional impact of the two TFs on Rh6 transcription was validated using the dual luciferase reporter assays and yeast one-hybrid (Y1H) assays. RNA interference (RNAi)-mediated knockdown of the TFs resulted in significant downregulation of Rh6 expression. Furthermore, silencing of BmHmx eliminated the preference for green in B. minax, while knockdown of BdPtx1 in B. dorsalis led to the loss of yellow preference. Our results elucidate the mechanism underlying transcriptional regulation of Rh6 towards color preferences in tephritids, which also provide new insights into the links between host location and visual ecology in insects.