Rhagoletis pomonella (Walsh) and Rhagoletis zephyria Snow (Diptera: Tephritidae) both occur in the U.S. Pacific Northwest and are frequently confused with one another due to their morphological similarity. The apple maggot, R. pomonella, is a threat to commercial apples [Malus domestica (Borkh.) Borkh.] in the Pacific Northwest, whereas R. zephyria attacks snowberry (Symphoricarpos Dill. ex Juss) and is not considered a threat. Configuration of the surstyli in males is used to discriminate between species, but this character shows overlap. In this study, we reexamined surstyli configurations in the two species. We then used geometric morphometrics to test the hypotheses that shapes of surstyli and of aculei between the two species differ and that combining aculeus shape and size measures improves discrimination. We found that all R. pomonella had an inwardly curved surstyli configuration (based on a ratio of width across bases of prensisetae to width between the outer edges of the surstyli near their ends), whereas R. zephyria included specimens having either a parallel or divergent configuration. Using canonical variates analysis, multivariate analysis of variance, and an assignments test, we found that surstylus shape classified 99.8% of males correctly to species. Aculeus shape accurately classified 85.3% of females to species. Combining aculeus shape and length increased classification accuracy to 94.5%. Within species, surstylus and aculeus shape did not discriminate among fly populations from different host fruit, collection areas, or both. Use of surstylus shape would benefit regulatory agencies that depend on accurate identifications of R. pomonella for quarantine and management measures.