Origanum ayliniae Dirmenci & Yazici, which differs significantly from O. dictamnus L., is described for the first time in this paper. In addition, a new hybrid, O. x adae Dirmenci & Yazici, between O. ayliniae and O. sipyleum L., is described and investigated in detail. The general morphology, pollen structure, chromosome features, and nuclear (ITS) and chloroplast (rpl32) genomes of collected specimens were studied. O. x adae was determined to have some intermediate properties morphologically and palynologically that place it between the parents. Pollen size and shape were important features in the diagnosis of the hybrid and its parents in this study. The somatic chromosome number of O. ayliniae, O. x adae, and O. sipyleum was counted as 2n = 30. According to the results of these different approaches, O. ayliniae differs significantly from O. dictamnus, which has a close relationship with O. ayliniae, and O. x adae has a hybrid nature. These results support previous reports for the speciation of Origanum members via hybridization. This study aimed to present a new species (O. ayliniae), a new hybrid of O. x adae, and their differences. In conclusion, O. ayliniae, O. x adae, and O. sipyleum provide significant morphological, micromorphological, palynological, cytological, and molecular information about homoploid hybridization.