Abstract：Employing fluorescent AFLP marker, we analyzed population genetic diversity and genetic structure of wild Pyrus ussuriensis with the aim to provide scientific foundation for wild Pyrus ussuriensis germplasm conservation and utilization. 90 accessions from Hailin, Dongning and Sunwu country of Heilongjiang province were selected as the research material. The results showed that the percentage of polymorphic loci (P) was 82.95% at species level, Nei's's gene diversity (H) was 0.1467 and Shannon information index (I) was 0.2397. And the genetic diversity of wild Pyrus ussuriensis Maxim was low. The polymorphic loci (P), Nei’s gene diversity (H) and Shannon information index (I) at population level were sequenced from high to low as Dongning population＞Hailin popultion＞Sunwu population, which means that genetic diversity of Dongning population is the richest in the three populations. The genetic differentiation coefficient (GST =0.1008) of the three populations showed that genetic variation mainly occurred within populations. There was higher level of gene flow between three populations (Nm=4.4603) which indicated that there were frequent gene exchange between populations. The UPGMA cluster analysis indicated that three populations are mendelian relative independent population, and the closer genetic relationship exist between Hailin and Dongning population. Dongning population has the most abundant genetic diversity and is the preferential population for the implementation of situ germplasm conservation strategies.