In this study, we sought to identify primary pears species and Korean native pears, without the use of morphological characteristics. In addition, this study was to establish pear DNA fingerprinting data for Korean native pears using 12 microsatellite markers, and to accurately classify a database for management of the Korean pear collection. Forty two pear accessions (7 primary pears, 5 Asian pears, 29 Korean pears, and 2 reference pears) were analyzed with twelve primers covering whole pear genome. In the present study, all pear accessions were successfully classified along with their pedigrees, and the distribution of primary pears was parallel to those of the previous taxonomic results. Korean pears were divided into 3 groups. Group I was characterized by Pyrus calleryana, and included Korean pea pears. Group II was characterized by P. pyrifolia, and was classified into 2 small groups. The first small group comprised of ‘Najucheongbae’, ‘Sunchanggulimdolbae’, ‘Andongmookbae’, ‘Andongdangsilri’, and ‘Najucheongbae’ and was presumed to be cultivars of P. pyrifolia. The second small group consisted of ‘Cheongdangrori’ and ‘Pyeongchangsuhyangri’. These two accessions were assumed to be a hybrid of P. pyrifolia and the other cultivar. Group III was characterized by P. ussuriensis. ‘Goesanhwangbae’, ‘Andongcheongsilri’, ‘Gongjucheongsilri’, and ‘Yecheoncheongbae’ were assumed to be cultivars of P. ussuriensis. Contrary to ‘Ulreungdocheongbae A’, ‘Ulreungdocheongbae B’ was classified as belonging to the P. ussuriensis group. It is possible that this is a consequence of, P. ussuriensis genes being transferred into ‘Ulreungdocheongbae B’. The result of this research reaffirmed the efficiency of a standard set of microsatellite markers and provides data, which will be useful for developing a core collection of pears.