This study was conducted to investigate the environmental characteristics of natural habitats, and the genetic variations in samples from 19 different quadrates of Asplenium scolopendrium 10 habitats. The natural habitats of A. scolopendrium were located at an altitudes 110-973 m with inclinations of 7-30˚. All the quadrates were located on north facing slopes. The average field capacity of the soil is 31.4%, with organic matter at 16.7%, and the pH is 5.84. The soil texture was confirmed as sandy loam in 8 habitats and silt loam in 2 habitats. A total of 214 vascular plants were identified from 10 habitats. The importance value of the herbaceous layer (H) was the highest in A. scolopendrium, at 10.4%, followed by Arachniodes standishii (7.3%), Dryopteris crassirhizoma (6.5%), and Polystichum tripteron (5.3%), which implies that the natural habitats of A. scolopendrium are affinity with ferns. The species diversity of A. scolopendrium was estimated as on average 1.09, while the dominance and evenness were 0.12 and 0.87, respectively. The result of the RAPD analysis, among 59 bands amplified with a primer, 25 (42.4%) showed polymorphism. Twenty-one individuals of 10 habitats could be classified into four groups with similarity coefficient values ranging from 0.74 to 1.0. Mt. Mullae and Geumdaebong populations shows basal branching within the 21 individuals. Ulleung-do island and Jeju-do island population forms an independent clade, respectively. Mt. Moak and Byeonsan-bando clade formed a sister to the Ulleung-do island and Jeju-do island clade.