A simple method of marking Mediterranean fruit fly Ceratitis capitata (Wiedemann) using stable isotopes is described. This species is economically important and is a target species of many successful area-wide integrated pest management (AW-IPM) programs using the sterile insect technique (SIT). Program monitoring in the field relies on being able 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 fluorescent dust, 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 caused by discrimination against the heavier isotopes during some biological processes. 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. The majority of fruit fly species feed on C3 plants in the wild, which have a carbon isotope signature of around -28‰. However, almost all mass-rearing facilities use cane sugar in the larval and adult diet, which is a C4 sugar source (with a signal of around -11‰), and this could provide an easy signature to differentiate released flies from wild flies. To test this approach, samples of flies from several mass-rearing facilities and wild populations were analyzed. It was clearly shown that using C4 sugar in the larval-rearing diet was an effective and economic way of intrinsically labeling Mediterranean fruit flies, and it was possible to distinguish mass-reared from wild populations with >95% confidence. The C4 marker was detectable and distinguishable from wild populations up to 12 d after “release.” This technique could be adopted for use in any other SIT program with similar rearing protocols to Mediterranean fruit fly.