Abstract: Genetic diversity of 114 isolates of Stylosanthes spp of Colletotrichum gloeosporioides in Hainan, Gunagdong and Guangxi was analyzed by use of random amplified polymorphic DNA (RAPD) and 8 arbitrary 10-base oligonucleotide primers. The amplified fragments were 0.2-3.0 kb. A total of 786 well-replicated, clear and stable bands were amplified by use of the primer CW38114. The results showed good DNA polymorphism between isolates. Four significant common bands were found between 260 and 650 bp in the amplification profile. However, between 650 and 3 000 bp showed large differences. The grouping analysis showed all the isolates grouped in four clusters, and clusters I and III could be divided into two subgroups each. The genetic variation differed by provinces: Hainan > Guangxi > Gunagdong. These isolates also showed parasitic specialization to some extent.