Yellow starthistle, Centaurea solstitialis L. (Asterales: Asteraceae), has invaded over 8 million ha of the United States and has been the target of biological control since the 1950s. In North America seven insect species were intentionally released as biocontrol agents, and one was accidentally introduced into the western United States. Two introduced fruit fly species (Diptera: Tephritidae), the yellow starthistle peacock fly, Chaetorellia australis Hering, and the false peacock fly, Chaetorellia succinea (Costa), attack Ce. solstitialis seedheads as immatures. Separation of the immature stages of these two flies in infested seedheads is difficult without rearing the adults. The puparial exuviae of these flies are retained in the seedhead for months following adult fly emergence, so they may be useful in forensic species diagnosis if differentiating characters exist. In this study, the vacant puparial exuviae of C. australis and C. succinea were evaluated using scanning electron microscopy to assess morphological differences between these species. It was found that the clusters of branched posterior spiracular hairs retained on the puparial exuvia can be used diagnostically to separate the two species: C. succinea has 5.91 ± 1.05 and C. australis has 2.67 ± 0.87 spiracular hair branches between the posterior spiracles. These differences provide a diagnostic tool that expands monitoring capabilities for the two important biological control agents.