Through repeated interspecific hybridization and backcrossing, genetic introgression, where parts of the genome are transferred, is a mechanism that enables rapid environmental adaptation. In the case of the cold-adapted species, Japanese stone pine (Pinus pumila), belonging to the pine genus, which thrives in vulnerable timberline ecosystems susceptible to global warming, introgression is believed to have played a crucial role in the adaptation to the rapid climatic changes during glacial and interglacial periods. P.pumila in Japan are known to undergo permeative hybridization with Kitagoyo (Pinus parviflora), a closely related species that thrives in warmer environments at lower elevations. Revealing the functions of the genes that introgressed from P. parviflora to P. pumila allows for predictions and assessments of the vulnerability and future adaptability of P. pumila to global warming. However, due to the substantial genome size of the pine genus, which is 25 Gbp, analyses of a few organelle and nuclear markers have been the primary focus in previous studies on introgression between these two species. In this study, we conducted exome-wide sequencing to obtain genome-wide functional gene sequence data. We prepared RNA-seq libraries from one individual each of P. pumila and P. parviflora collected in Mt. Hakkoda, Aomori Prefecture, and created capture probes. Shotgun sequencing libraries were prepared from 78 individuals of P. pumila and P. parviflora collected in the elevation range of 750 to 1580 meters on the same mountain. Using the created capture probes, we performed exome capture and sequencing, obtaining information on 17,000 SNPs (2.8 Mbp, 1600 loci). The population structure analysis revealed a pronounced bias toward P. pumila in the parental individuals involved in backcrossing beyond F1 in the hybrid population. Such hybridization patterns could be explained by light acquisition competition with surrounding vegetation. We delve deeper into Gene Ontology analysis of the estimated introgressed regions using statistics and integrate ecological information from P. pumila and P. parviflora. This integration enables us to discuss the evolutionary and ecological significance of interspecific hybridization.