Ribosomal ITS1 DNA sequences have been characterized in Ceratitis capitata (Weidemann), the Mediterranean fruit fly, and Ceratitis rosa (Karsch), the Natal fruit fly. In C. capitata the ITS1 region is 831 bp in size (on average). Relatively little variation in the makeup of the ITS1 DNA sequences was detected in individuals sampled from numerous worldwide populations of C. capitata. In C. rosa, however, a substantial difference in the size of the ITS1 region was observed in individuals from a collection made in Kenya compared with individuals from South Africa. In the C. rosa flies from South Africa, this region was ≈930 bp in size, compared with a size of 717 bp in the C. rosa Kenya flies. This difference appears to be due primarily to a single insertion or deletion event. Using polymerase chain reaction, these size polymorphisms are easily detectable and can be used for making species identification and/or population origin determinations using material from any stage of the life cycle. Despite these intra and interspecific differences, sequences from the ITS1 regions of both C. rosa collections and C. capitata can still be aligned. Quantification of the similarity of these sequences may help to resolve continuing questions over the status of species relationships in this genus.