Abstract: Tertiary relic temperate tree species Acer pictum is excellent to study evolutionary history in East Asia．Abundant morphological variations exist in this species, contributing to controversial classification at the species and subspecies level．Therefore low-copy primers with clear mutation mechanism and high diversity are of great significance in the evolution and taxonomy of A. pictum．In this study, we designed 166 pairs of primers based on transcriptome data, and screened for low-copy genes by agarose gel electrophoresis and Sanger sequencing．A total of 26 pairs of low-copy primers were used．Effectiveness of primers was verified by amplifications in 182 individuals of 63 populations in East Asia．Nucleotide diversity was found to range from 1.90×10⁻³ to 18.03×10⁻³, haplotype diversity from 0.45 to 0.97．Nine to fifteen pairs of primers were used for successful amplifications in Dipteronia sinensis, Acer ginnala, A. davidii and A. palmatum．STRUCTURE clustering data were found similar to previous nuclear microsatellite studies and showed more phylogenetic geography．Transcriptome data provided important genetic information for Acer, the method was effective．The 26 pairs of primers will provide rich and effective molecular markers for the study of evolutionary history of A. pictum and the phylogeny of Acer．