Genetic variation was found between isolates of Botrytis elliptica from the USA and Taiwan based on 22 polymorphic markers from five RAPD primers. Among these 69 isolates, there were 43 different genotypes. One clonal genotype was found spanning Oregon and Washington, USA, and in a population from Hsinshe, Taiwan, clonal genotypes were frequent, demonstrating the importance of asexual spread of this pathogen. However, when only unique genotypes were considered, gametic disequilibrium among putative RAPD loci of the genotypes from Taiwan (33) or Hsinshe (23) was not detected, suggesting an underlying sexual recombination system for this population of B. elliptica. A weak level of cultivar specialization was detected among B. elliptica isolates from the Hsinshe population based on analysis of genetic distances between isolates.