A new molecular marker has been developed to clarify the status and systematic relationships of forms within the Bactrocera tau (Walker) taxon. The B. tau taxon, previously described as a widely distributed species, has recently been subdivided into forms A, B, C, D, E, F, G, and I based on host-plant preferences, cytological differences and external morphologies. This new molecular marker is derived from the sequence of the heat shock protein 70 cognate gene Bthsc1. Fragments of this gene were analyzed from B. tau individuals representing each of the different forms. Patterns of sequence variation revealed that the average genetic distance measurement within the B. tau form A is significantly smaller compared with the other B. tau forms. Unweighted pair-group method with arithmetic average and neighbor joining analyses both indicated that B. tau form A individuals derived from various geographical populations may be reliably separated from other forms B, C, D, E, F, G, and I. Our results also show that the Bthsc1 marker may successfully resolve other relationships among these forms. For example the B. tau forms B, F, and G, which are monophagous on related host plants, also cluster together as a closely related group.