Abstract: This experiment aimed to provide the basis for molecular identification and genetic diversity of Amygdalus communis L. germplasm resources in Xinjiang. This experiment used 24 germplasms of Amygdalus communis L. as the materials, PCR amplification and sequencing of the ITS sequence were carried out after extracting DNA. The sequencing results were compared with KC862380 (Prunus lusitanica var.), and then ITS1, 5.8S and ITS2 sequences were obtained. Then the authors used relevant bioinformatics software to calculate the mutation sites and simple information sites, etc. of ITS1 and ITS2 sequences. The UPGMA phylogenetic tree was built. The results showed that, after being aligned, the sequence length of ITS1 and ITS2 were 230 bp and 277 bp, respectively, and they had rich mutation sites and simple information sites. Based on ITS1, the genetic distance of UPGMA phylogenetic tree was 0.00-0.01, ‘Yingzui’, ‘Aifeng’ and ‘Shizi’ were divided into respective branch. Based on ITS2, the genetic distance of UPGMA phylogenetic tree was 0.000-0.006, ‘Yingzui’ and ‘Shizi’ were divided into the same branch. This test showed that 5.8S rDNA sequence had strong conservation. The variation information of ITS1 sequence was greater than that of ITS2 sequence, and the bases lack and replace phenomena of ITS1 sequence were more than those of ITS2 sequence, which might be the reason of phylogenetic tree differences.