Protein expression patterns were compared in mussels from a hybrid zone between the two species Mytilus edulis and M. galloprovincialis using 2-DE. Significant differences in expression pattern were observed between species and between mussels within species. Hybrid mussels had more variable protein expression patterns than mussels of each species. This could be due to segregation at expression modifier loci in the hybrids. It is proposed that unusual hybrid expression patterns might contribute to postzygotic isolation, if such patterns reduce fitness. The use of proteomic data for testing evolutionary models, as in many transcriptomics studies, is explored with results consistent with the expectations of neutral theory.