Cytotype distribution, B-chromosome frequency, and genomic constitution in the natural populations of the Scilla scilloides complex in Korea were analyzed. Plants with various cytotypes were found: AA (2n=16), BB (18), AAB (25), ABB (26), ABB (34), ABBB (35), BBBB (36), AABBB (43), AAABBB (51) and AAAABBBB (68). Allotetraploid AABB plants predominated with a frequency of 68.3%, and were found to distribute all over the Korean peninsula and Cheju-do. In diploids, the type AA plants distributed throughout the Korean midwest, while the type BB plants were limited to Cheju-do. Two other cytotypes, ABBB and AABBB, were found only in the southern part of the Korean peninsula including Cheju-do. Chromosomal variations, aneuploidy, and centromeric shifts were also found in the natural populations. The cytotypes AAB and AAAABBBB are reported here for the first time. B-chromosomes were found in 149 (85.6%) of 174 populations, the highest frequency being 81.8% in BB populations. The number of B-chromosomes per plant ranged from 1 to 31, and 1B plants predominated (21.0%). Subtypes, with respect to the number and composition of B-chromosomes, indicated that sexual reproduction is still prevalent in AABB populations.