RAPD analysis showed that all the OTUs of 'Sandolbae' were the same species because amplified band patterns of all samples generated by each of 5 random primers were identical. Even though there were different environmental conditions, all the "Chuiangne" trees from three different places were the same species, and also all the "Cheongshilli" trees were the same species too. No genetic variations were detected between native Korean pears grown in the habitats and in the research field. Because 212 polymorphic bands were generated by 9 primers selected through primer screening, they were possible to analyze genetic relationship among naturally growing three native Korean pears and nine cultivars of Pyrus pyrifolia and P. communis. Based on the RAPD analysis, three main groups were formed. The first group represented the Six P. pyrifoia cultivars, the second group was the three native Korean pears, and the last group was the three P. communis cultivars. Genetic distance between 'Wonwhang' and 'Chojuro' was closer than other cultivars in group 1 since dissimilarity index value between these two cultivars was 50.82. However, genetic distance between 'Niitaka' and 'Chojuro' was the most distant compared to the others in group 1. In group 2, 'Sandlobae' was genetically closer to 'Chuiangne' than 'Cheongshilli' because dissimilarity index value between 'Sandlobae' and 'Chuiangne' was smaller, 50.82, than the value between 'Sandlobae' and 'Cheongshilli', 63.636. In group 3, 'Old Home' was genetically closer to 'Bartlett' than 'Kaiser Alexander(or Bosc)'. Group 3 composed of P. communis cultivars was genetically further than other two groups, P. pyrifolia cultivars and native Korean pears.