We consider here the possibility of using III-V heterostructure nanowires as electrodes for molecular electronics instead of metal point contacts. Using ab initio electronic structure and transport calculations, we study the effect on electronic properties of placing a small molecule with thiol linking groups, benzene-di-thiol (BDT), within a nanosize gap in a III-V nanowire. Furthermore, it is investigated how surface states affect the transport through pristine III-V nanowires and through the BDT molecule situated within the nanogap. Using GaAs and GaP as III-V materials we find that the BDT molecule provides transport through the entire system comparable to the case of gold electrodes.