Wild congeners of cultivated fruit trees are vital sources of genetic diversity for crop improvement and key targets for conservation. However, cultivating crops within the range of rare wild congeners increases the risk of interspecific hybridization, threatening the genomic integrity of wild species. This is a concern for Pyrus in Central Asia, where a critically endangered wild species, P. korshinskyi, coexists with cultivated Pyrus communis and another widespread species, P. regelii, forming a species complex in which species boundaries are unclear, complicating conservation efforts. Here, we sought to assess: 1) the distinctiveness of species, 2) the extent to which interspecific hybridization and introgression may reduce the genetic integrity of P. korshinskyi, and 3) genetic diversity and structure within P. korshinskyi.  Using RAD sequencing to genotype 185 individuals from 13 presumed wild and ex situ populations in Kyrgyzstan, we found that P. korshinskyi is genetically distinct, highly morphologically variable, but occasionally hybridizes with both P. regelii and P. communis. Morphometric analyses indicate that the parental species and hybrids can be differentiated based on leaf characters. Unexpectedly, several reportedly wild populations of P. korshinskyi were found to be clonally propagated; unfortunately, because Pyrus exhibits gametophytic self incompatibility and all of the trees are the same genotype, these propagated populations are mate limited, limiting their conservation value. While P. korshinskyi populations are genetically diverse, further efforts are needed to preserve wild genetic diversity ex situ. These findings guide conservation strategies to maintain genetic integrity and diversity of P. korshinskyi both in situ and ex situ, underscoring the importance of genetic analyses for conserving crop wild relatives, especially in complex cultivated-wild mosaics.