Premise of research. Spontaneous hybrids between species of Rosa sect. Caninae represent a unique example to study the genetic and epigenetic consequences of an imbalanced parental contribution to polyploid hybrids. Due to the unique canina meiosis, pentaploid or hexaploid dog rose hybrids contain a single subgenome transmitted by the haploid pollen grain of the paternal species and four to five subgenomes transmitted by the tetraploid or pentaploid egg cell of the maternal species. During this study, we investigated epigenetic changes in spontaneous reciprocal hybrids between the subsections Caninae and Rubigineae compared to their parental species in a natural population in eastern Germany.Methodology. For investigating epigenetic patterns, we applied cDNA–amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs). Additionally, we analyzed microsatellite data and measured morphological characters.Pivotal results. In line with expectations deduced from the genetic composition of the pentaploid and hexaploid hybrids, we observed a maternal bias of DNA methylation and expression patterns. We did not detect silencing of the respective paternal subgenomes. However, the percentage of paternally expressed fragments differed between plant organs. We found a higher number of paternally expressed fragments in sepals compared to leaves, suggesting that the parental genetic information underwent a rapid subfunctionalization in recently formed hybrids. Moreover, epigenetic data obtained from cDNA-AFLPs and MSAPs correlated stronger with morphology than with genetic data, based on microsatellites.Conclusions. The genetic contribution of subgenomes is strongly biased toward the maternal parent in dog rose hybrids, leading to a nearly apomictic mode of inheritance. However, we found that the underrepresented paternal genome is not silenced but transcribed and differentially expressed between plant organs. The correlation between epigenetic data and morphological data implies that the probably fast-evolving epigenetic changes have a major impact on dog rose phenotypes and may affect the establishment of hybrids in natural populations.