Cytogenetic analyses were done in thirteen natural populations of Scilla scilloides complex collected from Chejudo. Six genotypes, BB (2n=18), ABB (2n=26), AABB (2n=34), ABBB (2n=35), AABBB (2n=43) and AAABBB (2n=51) were observed, where A and B denote genomes with x=8 and x=9, respectively. Genotypes BB, ABB and AAABBB were found for the first time in Chejudo populations. Genotypes BB and ABB were never reported from the Korean populations. Six of the populations investigated were mixed populations of two or three cytogenetic types, and others were pure populations consisting of BB (1), AABB (4) and AABBB (2). AABB genotypes were predominant over other genotypes and AABBB was the next. AA genotypes growing in the mainland of Korea was not found. It was suggested that the Chejudo populations of S. scilloides complex were closely related to the Japanese populations than mainland populations of Korea. The number of B-chromosome ranged from one to four. The B-chromosomes were all isochromosomes (F) and no chromosome fragment (f) was found. The frequencies of B-chromosome were 75% in BB and AABBB genotypes, respectively. The frequency of B-chromosome in AABB plants was similar to that of AABB plants reported in the mainland populations.