Morphological and RAPD features of Ceramium kondoi populations were investigated and compared in different locations in Korea. The plant length and branching pattern were more variable in Jindo population than others. RAPD data showed that C. kondoi planats were divided into two clades; the southern group including Jindo and Bangpo population, and the northern group including Yonpyongdo and Oeyondo population. Morphological features in C. kondoi populations corresponded with RAPD data, which differed from those of C. boydenii from the same location. These results suggest that RAPD might be useful for elucidating genetic variation among the wild populations of C. kondoi.