Chrysanthemums have beautiful flowers with high ornamental value and rich genetic diversity. Amplified fragment length polymorphism (AFLP) markers were used to detect the relationships among 12 wild accessions and 62 groundcover chrysanthemum cultivars. Nineteen EcoRI/MseI primer combinations revealed 452 informative polymorphic bands with a mean of 23.8 bands and 71.5% polymorphic rate per primer pair. Jaccard’s coefficient of similarity varied from 0.64 to 0.89, indicating much genetic variation in chrysanthemums. The 74 accessions were classified into two major groups by unweighted pair group method with the arithmetic averages (UPGMA). The dendrogram showed that AFLP variability was closely correlated with both geographic distribution and traditional classification of the wild accessions. Among all accessions, genetic relationship was the most relevant factor in AFLP-marker clustering, whereas petal type was also informative. AFLP technology could be very efficient for discriminating species of chrysanthemum and its related genera and reconstruct their genetic relatedness.