Medicinal and aromatic plants (MAPs) belonging to the genus, Origanum L. (Lamiaceae), are called “oregano”. They are economically important and beneficial for trade, medicine, food, cosmetics, and ornamental purposes with their bioactive compound diversity and richness. Although Türkiye is the gene center for generation, speciation, and diversification of oregano throughout the world, their uncontrolled consumption and other factors threaten their status. According to Ietswaart (1980), there are ten morphological sections in the genus. Of these, 25 taxa (including 13 endemics) and 13 hybrids from eight sections grow naturally in Türkiye. The cross-pollinating and gynodioecious nature of oreganos makes their taxonomic classification difficult. In this dissertation, molecular markers (EST-SSRs and SRAPs) were used to assess the complex evolutionary relationships in a herbarium and the Turkish national AARI Gene Bank collection. Cross hybridization due to high gene flow was found to be the main source of genetic diversity within both collections. In both collections, the highest gene flow was observed between two sections, ANA and BRE, with diecious flowers which supports their frequent hybridization when compared to gynodioecious oreganos in nature. The Aegean and Mediterranean regions had the highest gene flow among all regions, while five province pairs had the highest gene flow among all provinces. In conclusion, molecular markers were shown to be a useful tool for examinations of genetic diversity and evolution in oregano.