Abstract: Genetic variants in Vitis davidii from Fuan District in Fujian were studied using the high-throughput genome sequencing method. The 8.4 Gb of raw data were analyzed to result in the identification of 3 192 484 non-redundant genetic variants. Distribution of the variants showed 30.34% in the intergenic regionand 3.67% in the exon region. By comparing the genome sequences of the V. davidii under study with those of the entire grape references, 1 863 237 homo-type SNP and 1 244 590 hetero-type SNP were found. It appeared that the V. davidii from Fuan were most likely to be allodiploidy. The study also indicated that using genetic sequencing to determine the genome-wide variants of V. davidii was a viable tool for better understanding of the genetic background of the plant in question.