Not only were used Random amplified polymorphismic DNA (RAPD) markers as input for an analysis of molecular variance (AMOVA) and cluster analysis to describe the population genetic structure, but also morphometric analysis of Formica japonica in Korea in order to investigate the relationships between local populations according to altitude. The ten populations of F. japonica in Korea did not showed any relationships according to altitude in morphological analysis, while they showed distinct relationship in RAPD analysis. It was noticed that they were clearly separated as four groups according to altitude. The first was Jirisan-Gachilbong-Gyebangsan population, the second Iksansi-Odongdo, the third Deukyusan-Hallasan, the fourth Siheungsi-Seonamsa-Jinjusi. The first group was high mountainous, the second flat and low altitude, the third high mountainous, and the fourth flat and low altitude. They occur from low altitude to comparative high altitude 1,400 m in Korea. Actually, it was found that the relationships of 10 local populations of Korean Formica japonica were not related to morphological evolution, but related to molecular evolutionary data evolved from RAPD analysis.