Abstract: AFLPs and SSRs were compared in terms of their efficiency in studying the genetic relationship of 41 Malus species. Genetic relationship among 41 Malus species was analyzed by AFLP, SSR technique and AFLP+SSR. 7 primer pairs were selected from 64 AFLP primer pairs, and 7 primer pairs selected from 40 SSR primer pairs. The average polymorphic rate of 7 pairs of primers was 86.72% and 100.00%. UPGMA clustering analysis indicated that the 41 Malus species could be divided into 6 categories separately using the three methods, which were similar to the traditional classification methods. Some new found apple species were identified and clarified, the accuracy of the three methods were compared. The cluster results showed AFLP technique had higher consistency with traditional classification and field performance than SSR and AFLP+ SSR. The results provided molecular basis for classification of Malus germplasm resources.