Abstract: ITS and matK sequences of 69 A. crenata samples collected from 16 populations were sequenced in both directions and spliced. Genious 11.0 was applied to analyse the structural variation of the 2 sequences, and MEGA 11.0 software was applied to calculate the genetic distance between the seed sources based on the Kimura-2-Parameter（K2P） model, and the neighbour-joining（NJ） method was used to construct phylogenetic trees respectively. Results showed that ITS and matK sequences of A. crenata were from 447 bp to 451 bp and from 844 bp to 861 bp in length respectively, with GC contents from 55.30% to 56.3% and from 33.70% to 34.4% respectively, 24 and 43 variant loci respectively, haplotype diversity of 0.947 and 0.917 respectively, and nucleotide diversity of 0.013 14 and 0.006 0 respectively. The genetic distance between populations of A. crenata ITS sequences ranged from 0.000 4 to 0.032 0, with a mean genetic distance of 0.018 4; the genetic distance between populations of matK sequences ranged from 0.000 0 to 0.019 6, with a mean genetic distance of 0.008 6. The phylogenetic results showed that both ITS and matK sequences clustered 16 populations of A. crenata into 2 branches with small genetic distances. Study showed that, A. crenata from different populations had a relatively rich genetic diversity and the genetic distance was related to the geospatial distance of the populations. The ITS was richer in variation than the matK sequence and was more suitable for studies on the genetic diversity and molecular marker development of A. crenata.