Abstract: We studied the SNP locus and candidate genes closely related to the red leaf traits of Eucommia ulmoides ‘Hongye’ for further revealing the genetic basis and molecular mechanism of red leaf traits. We used E.ulmoides ‘Hongye’ and the common green leaf E.ulmoides to perform whole genome sequencing with a depth of about 10x. With resequencing data and by using SnpEff software we predicted the effect of mutation sites on protein coding, selected the differential sites associated with the formation of E.ulmoides ‘Hongye’ leaf color, which were related to anthocyanin metabolic pathways and key enzyme genes. For fine mapping, 14.16 Gb clean data were generated from genome re-sequencing of E.ulmoides ‘Hongye’ and 14.29 Gb of clean data was produced by E.ulmoides ‘Xiaoye’. There are 1 516 SNPs in the E.ulmoides ‘Hongye’ which have serious effects on protein function, and 41 328 moderately affected. There are 1 640 SNPs in the E.ulmoides ‘Xiaoye’ that seriously affect protein function, and 47 192 SNPs that moderately affect function. Of the 26 722 genes, 228 were found to be involved in the synthesis of anthocyanin or flavonoids. After screening, 12 specific SNP loci were identified, all of which belonged to missense mutations in the exon region. Using a generation of sequencing verification, 7 pairs of primers were designed based on the SNP position, and the SNP accuracy rate reached 100%.