Despite an increasing acceptance in the biological community for sympatric speciation as a mode of species formation, well documented examples of sympatrically evolved ‘incipient species’ remain rare. The sympatric host races of apple maggot, Rhagoletis pomonella (Walsh), represent one of the most prominent case studies for sympatric speciation via a host shift. The European cherry fruit fly, R. cerasi (L.), shows strong ecological similarities to R. pomonella: (1) infestation of two different host plants, Lonicera xylosteum L. and Prunus avium L., and (2) divergent phenological and behavioral adaptations of flies on different hosts. The population genetic study presented here addresses whether the host associated populations of R. cerasi also represent genetically differentiated true host races. Out of a total of 29 allozyme loci examined, six were polymorphic and used to analyze six sympatric pairs of R. cerasi populations on Lonicera and Prunus from Switzerland and Germany. A direct comparison of allele frequencies between sympatric sites showed no pattern indicative of host races in R. cerasi. However, the hierarchical F‐statistic for one locus, mannose 6‐phosphate isomerase (Mpi), showed significant population differentiation that was in accordance with host race differentiation. Mpi is one of several loci that are also diagnostic for host race differentiation in R. pomonella. Results from Mpi suggest the formation of sympatric host races in R. cerasi, but additional polymorphic markers are necessary.