Rhagoletis pomonella (Walsh) (Diptera: Tephritidae) is a quarantine pest of apple (Malus sp.) in Washington state that is almost identical morphologically to Rhagoletis zephyria Snow, a nonpest of apple. Historically, the longer ovipositor in R. pomonella has been used to separate it from R. zephyria, despite overlap in ovipositor lengths. Here, the objectives were to determine whether use of multiple body measurements and wing shape can improve discrimination of the species. Ovipositor lengths allowed 94.6% correct identification of female R. pomonella but only 7.0% correct identification of R. zephyria. We found that multiple body measurements and wing shape can better separate these species. Canonical variates analysis (CVA) of nine body measurements in female flies largely separated the species. In contrast, CVA of nine body measurements poorly separated the males of these species. Discriminant analysis using nine body measurements classified female R. pomonella and R. zephyria with 95.4 and 100% accuracy, respectively. Geometric morphometrics and CVA separated wing shapes between species in both sexes. Bookstein shape coordinates indicated that the wing of R. pomonella is more tapered at the tip than that of R. zephyria. Use of wing shape in an assignments test identified female R. pomonella with 98.5% and female R. zephyria with 99.0% accuracy, and it correctly identified 100% of flies whose identities were questionable based on ovipositor lengths. Results indicate that use of multiple body measurements or wing shape is an improvement over the use of ovipositor length alone for identifying female R. pomonella and R. zephyria in Washington state.