The AFLP technique (amplified fragment-length polymorphism) was employed to identify and isolate species specific markers in tephritids. We have found that the technique has good potential for this purpose, with the only difficult part being the reamplification of AFLP fragments from silver stained gels. Cloning of putative species-specific markers and genomic dot blot hybridizations resulted in the development of diagnostic probes for tephritid identification. A repetitive DNA sequence from the genome of Ceratitis capitata (Wiedemann) was isolated. This sequence rapidly and reliably identified C. capitata and C. rosa Karsch in a collection of closely related and outgroup species tested in this study. Although this probe has been developed for C. capitata and C. rosa, the proposed methodology can be applied to any group of organisms.