To study genetic variation in Acer pentaphyllum Diels, a total of 64 A.pentaphyllum accessions were collected from three sub-locations at Shade, and two sub-locations each at Jiulong and Yajiang, in Sichuan, P.R. China. They were then analysed by amplified fragment length polymorphisms(AFLPs).Dendrograms were constructed using the bootstrap(BS)and interior-branch(IB)tests. Clustering by the unweighted pair group method using averages(UPGMA)resolved all A. pentaphyllum accessions into one cluster,regardless of collection location. However, some accessions(eg.,Shade A2,A4,C2,and C7,and Jiulong A1 and B2)were clustered together with A. mono and A. davidii when dendrograms were construced with neighbour-jointing(NJ),minimum evolution(ME),or when each accession was assigned to a population analyed by STRUCTURE.This suggested that these accessions were genetically different from other accessions of A.pentaphyllum.However,sequence analysis of the ribosomal protein L16(rpL16) gene,the chloroplast tRNA-Leu gene,and the internal transcribed spacer regions of nuclear ribosomal DNA(ITS nrDNA)revealed no single nucleotide polymorphisms(SNPs)in any of these genes among all A.pentaphyllum accessions tested, regardless of collecting site(population).Analysis of molecular variance(AMOVA)revealed that most of the variation existed between individual plants at a particular sub-location. Both a narrow genetic base,and undesirable habitats for seed germination, and the establishment of young seedlings, could contribute to the small number and limied distribution of these plants in nature.