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The sterile insect technique has been successfully used to eliminate tsetse populations in a number of programs. Program monitoring in the field relies on the ability to accurately differentiate released sterile insects from wild insects so that estimates can be made of the ratio of sterile males to wild males. Typically, released flies are marked with a dye, which is not always reliable. The difference in isotopic signatures between wild and factory-reared populations could be a reliable and intrinsic secondary marker to complement existing marking methods. Isotopic signatures are natural differences in stable isotope composition of organisms due to discrimination against the heavier isotopes during some biological processes. As the isotopic signature of an organism is mainly dependent on what it eats; by feeding factory-reared flies isotopically different diets to those of the wild population it is possible to intrinsically mark the flies. To test this approach unlabeled samples of Glossina pallidipes (Austen) (Diptera: Glossinidae) from a mass rearing facility and wild populations were analyzed to determine whether there were any natural differences in signatures that could be used as markers. In addition experiments were conducted in which the blood diet was supplemented with isotopically enriched compounds and the persistence of the marker in the offspring determined. There were distinct natural isotopic differences between factory reared and wild tsetse populations that could be reliably used as population markers. It was also possible to rear artificially isotopically labeled flies using simple technology and these flies were clearly distinguishable from wild populations with greater than 95% certainty after 85 days of “release”. These techniques could be readily adopted for use in SIT programs as complimentary marking techniques.