The present study researched morphological characteristics and analyzed the genetic diversity by using RAPD in Calanthe species, native plant in Jeju, Korea. Twenty-six samples were selected by flower color, and 19 horticultural traits were investigated to study morphological characteristics. The C. discolor had the smallest leaf, the length and width of dorsal sepal, lateral sepal, petal, central lip, lateral lip, and flower stalk length were shortest and/or smallest except the spur and ovary length in Calanthe species, but those of Calanthe discolor for. sieboldii (Dence.) Ohwi (Calanthe discolor for. sieboldii) were the largest and/or biggest, and those of variants were the intermediate between C. discolor and C. discolor for. sieboldii, but spur length was the longest in C. discolor, the shortest in C. discolor for. sieboldii, and intermediate in the variants. Ovary length in C. discolor was shortest and C. discolor for. sieboldii and variants were similar with each other. The flower colors of C. discolor were brownish red, the value of CIE Lab was between 40 and 50. The flower color of C. discolor for. sieboldii was yellowish; the value of CIE Lab was between 110 and 130. And variants had various colors between 50 and 70 in the value of CIE Lab. After analyzing multiple band patterns of PCR products, 154 bands were selected as polymorphic RAPD markers. The analysis of Genetic distance of Calanthe species using RAPD showed that C. discolor and C. discolor for. sieboldii are more distant from each other than variants, and demonstrated the fact that genetic position of variants is between the other two species.