Hybridogenetic species possess a hybrid genome: half is clonally inherited (hemiclonal reproduction) while the other half is obrained each generation by sexual reproduction with a parental species. We addressed the question of whether different hemiclones of the hybridogenetic water frog Rana esculenta are locally adapted for genetic compatibility with its sexual parental host Rana lessonae. We artificially crossed R. esculenta females of three hemiclones (GUT1, GUT2, GUT3) from a pond near Gütighausen, Switzerland and one hemiclone (HEL1) from near Hellberg, Switzerland each to R. lessonae males from both populations. We also created primary hybrids by crossing the same R. lessonae males from both populations to R. ridibunda females from Poznan´, Poland (POZ). Tadpoles were then reared in the laboratory at two food levels to assess their performance related to early larval growth rate, body size at metamorphosis and length of the larval period. Tadpoles from hemiclones GUT1, GUT3 and POZ had higher growth rates than those from hemiclones GUT2 and HEL1 at the low food level, but at the high food level all growth rates were higher and diverged significantly between hemiclones GUT2 and HEL1. Tadpoles from the intrapopulational crosses GUT2 x GUT and HEL1 x HEL were larger at metamorphosis than those from the interpopulational crosses GUT2 x HEL and HEL1 x GUT. A high food level increased the size at metamorphosis in all tadpoles. A high food level also decreased the days to metamorphosis and tadpoles from GUT1, GUT3 and POZ had the shortest larval period whereas those from GUT2 and HEL1 had the longest. These results indicate that the differential compatibility of clonal genomes may play an important role in hybridogenetic species successfully using locally adapted sexual genomes of parental species and that interclonal selection is likely important in determining the distribution of hemiclones among local populations.