The brown alga Sargassum muticum (Yendo) Fensholt, a component of the native algal flflora of East Asia,is now one of the major macroalgal invaders of the coasts of North America and Europe. To investigate the genetic diversity of native populations, we analyzed mitochondrial cox3 and trnW-I from a total of 144 specimens of this species from Korea, Japan, as well as from North America, and Europe. A total often haplotypes were found in the concatenated cox3 + trnW-I dataset: seven in western Korea, four in southern Korea, one each in eastern Korea and Jeju, one in Japan, and one each in Europe and North America. Haplotype 1 was common in Europe and North America, as well as in Korea. The number of private haplotypes, and haplotype and nucleotide diversities, were higher on the west coast of Korea than on the other coasts. No private haplotype was found in invaded areas. Thus, the west coast of Korea may be a native genetic diversity center.