In this study, three hybrids of Origanum (Lamiaceae) were examined in detail using morphological, karyological, palynological and molecular approaches. One of the three hybrids, O. x aytacii, is here described for the first time, and is compared with its putative parents, O. sipyleum and O. vulgare subsp. hirtum. In addition to morphological, karyological and palynological features, we also examined nuclear ribosomal DNA (ITS) sequences of O. x intermedium (O. onites x O. sipyleum), O. x intercedens (O. onites x O. vulgare subsp. hirtum) and their purported parental species that share the same area with the new hybrid. Pollen grains were hexacolpate and isopolar. The range of Polar/Equatorial ratio (P/E) of pollen for investigated taxa varied from 0.74 to 0.99. All investigated taxa are diploid with a chromosome number as 2n = 30. According to molecular results, O. x aytacii was the most polymorphic taxon. In addition, DNA sequences showed that O. x intercedens was more similar to O. vulgare subsp. hirtum than to O. onites, and O. x intermedium was more similar to O. onites than to O. sipyleum. Furthermore, O. onites and O. vulgare subsp. hirtum have many different ITS haplotypes, probably resulting from backcrossing with different individuals. Results obtained in this study demonstrate that hybridization has played a major role in the process of Origanum speciation.