Under incomplete reproductive isolation, secondary contact of diverged allopatric lineages may form hybrid zones that allow to study recombinants over several generations as excellent systems of genomic interactions, resulting from the evolutionary forces, acting on certain genes and phenotypes. Hybrid phenotypes are expected to either exhibit intermediacy or, alternatively, transgressive traits, which exceed the extremes of their parents due to epistasis and segregation of complementary alleles. While transgressive morphotypes have been examined in fish, reptiles, birds, and mammals, studies in amphibians are rare. Here, we associate microsatellite-based genotypes and morphometrics-based morphotypes of two European tree frog species of the Hyla arborea group, sampled across a hybrid zone in Poland, to understand whether the genetically differentiated parental species also differ in morphology between each other and their hybrids, and whether secondary contact leads to the evolution of intermediate or transgressive morphotypes. Using univariate approaches, explorative multivariate methods (Principal Component Analyses) as well as techniques with prior grouping (Discriminant Function Analyses), we find that morphotypes of both parental species and hybrids differ from each other. Importantly, hybrid morphotypes are neither intermediate nor transgressive but found to be more similar to H. orientalis than to H. arborea. Our study presents one of the rare datasets, in which genotypes along with morphotypes examined the occurrence or absence of transgressive morphologies in wild amphibians.