Introduction Quince (Cydonia oblonga Mill.) is a pome fruit, like apple and pear, that belongs to the family Rosaceae. It originated in northern Iran, the Hazar Sea, South Caucasus, Khurasan, and Anatolia. Its fruit is mainly used by the food industry to produce jam, jelly, and marmalade. Quince is a good source of minerals, vitamins (especially vitamin C), and sugars (Bucsek et al., 1996) as well as flavonoid compounds, such as quercetin, rutin, and kaempferol (Silva et al., 2002, 2005). The total global production of quince has reached about 677,949 metric tons, and Turkey is one of the main producer countries, along with Uzbekistan and China, and is responsible for about 19% of the total global production (Faostat, 2016). In Turkey, most of the quince cultivars originated from seedlings accidentally grown in backyards or at the borders of orchards (Özbek, 1978). There are still many natural quince accessions in different regions of Turkey that are valuable genetic resources for quince breeding. All quince cultivars and accessions belong to one species in the genus Cydonia. Identification and characterization of quince accessions morphologically are considerably difficult due to high similarities in the tree structure and fruit traits of quince plants (Yamamoto et al., 2004). Identification of relationships based on morphological characteristics has been widely used in many species including walnut (Keles et al., 2014), cherry (Rakonjac et al., 2010), and olive (Cantini et al., 1999). However, morphological characterization does not perfectly reveal the relationship due to the influence of environmental factors and low heritability (Cadee, 2000; Bucheyeki et al., 2009). DNA-based molecular markers have been effective tools to characterize plant materials for the last several decades (Lacis et al., 2009). Simple sequence repeats (SSRs) are a marker of choice due to their codominant nature, abundance in the genome, suitability for automation, high polymorphism, and repeatability (Kacem et al., 2017). One of the main advantages of SSR markers is their transferability between closely related species (Schlotterer and Tautz, 1992). The use of SSR markers for molecular characterization is well proven in different species, such as apple (Gasi et al., 2016), apricot (Hormaza, 2002), peach (Bouhadida et al., 2007), pear (Fan et al., 2013), pistachio (Zaloglu et al., 2015), and walnut (Topcu et al., 2015). Therefore, the use of SSR markers to determine the relationships among quince accessions can be highly reliable.