Anthracnose pathogen can caus e worldwide anthracnose to many plants. The paper presents the population genetic structure of C. siamense strains isolating from thirteen host plants growing in four regions of Hainan. 95 ITS-CAL-GAPDH gene sequences of C. siamense could be defined as 16 haplotypes. And the major haplotypes H5 was found in the thirteen hosts. AMOVA analysis showed that the genetic variation mainly took place within the population. And the pathogen didn't experience large -scale population expansion. The results show...