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AFLP markers were employed to detect genetic diversity in two cultivated Perilla frutescens (i.e. var. frutescens and var. crispa) and their weedy types and to assess their genetic relationships. Analysis of 60 Perilla accessions from China, Korea and Japan by seven AFLP primer combinations identified a total of 125 fragments, of which 80 (64%) were polymorphic at the species level. The phenotypic diversity meassured by Shannon's index of information for the cultivated type of var. frutescens, the weedy type of var. frutescens, the cultivated type of var. crispa and the weedy type of var. crispa were on average 1.07, 2.23, 1.24 and 1.75, respectively. The weedy types exhibited high within-type variation in spite of a small number of samples. In the neighbor joining tree, two major clusters were recognized: (1) cultivated type of var. frutescens, (2) weedy type of var. frutescens, and cultivated and weedy types of var. crispa. The cultivated types of var. frutescens and of var. crispa were sharply separated by AFLPs. However, there remained ambiguities in regard to the intraspecific relaltionships, due to the clustering of the weedy types which occured in each of the clusters of the cultivated types. Two cultivated types of P. frutescens and their weedy types should be taxonomically considered as a P. frutescens complex. The present AFLP data are consistent with the hypothesis that China is the original place of cultivation of var. frutescens and Korea is a secondary center of diffusion of var. frutescens.