Isozyme analyses were conducted to study the geographic variation of Capsicum frutescens L. in Southeast and East Asia, and to investigate its dispersal routes into Japan. Eight enzymes (EST, FM, G6PD, GR, ME(A), PGI, PGM, ShDH) were variable among accessions of C. frutescens in Southeast and East Asia. Accessions from the Ryukyu Islands were closely related to those in Indonesia, whereas accessions from the Bonin Islands showed exactly the same isozyme patterns as those from Indonesia and Northern Thailand. Accessions in the Ryukyu Islands were different from those in the Bonin Islands, suggesting that there may be two independent dispersal routes into Japan. One route was from Indonesia via the Philippines or Taiwan, or directly to the Ryukyu Islands, and another was from Indonesia via the Mariana Islands, or other islands in the Pacific, to the Bonin Islands.