Stylosanthes guianensis, belonging to the genus Stylosanthes, is one of the most important tropical forage legumes and is native to South and Central America and Africa. Anthracnose, caused by the fungus Colletotrichum gloeosporioides (Penz.) Sacc., is a major constraint to the extensive use of Stylosanthes as tropical forage. Forty-two accessions of S. guianensis were assessed with amplified fragment length polymorphism (AFLP) for genetic diversity and for resistance to anthracnose. In AFLP analysis, four selective primer combinations screened from 96 primer combinations were used to analyse these accessions, and a total of 225 clear bands were used for genetic similarity (GS) analysis, showing a 95.5% level of polymorphism on average. GS from 31.0% to 95.0% among the accessions was calculated with NTSYS-pc software. The dendrogram was constructed with unweighted pair group method of averages (UPGMA) based on the AFLP data, and five clusters were defined at 48% GS. Two typical strains of C. gloeosporioides from Stylosanthes in China were used for anthracnose resistance screening. Most of the plant accessions showed variation in the reaction to two strains, and the correlation of resistance had a value of 0.904 (P < 0.01), suggesting common resistance to the two strains. The resistance accessions were randomly distributed in different groups of UPGMA clustering. These results demonstrate that AFLP analysis is an efficient method for evaluating the genetic diversity among S. guianensis accessions.