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Vitis riparia, a critically important Native American grapevine species, is used globally in rootstock and scion breeding and contributed to the recovery of the French wine industry during the mid-19th century phylloxera epidemic. This species has abiotic and biotic stress tolerance and the largest natural geographic distribution of the North American grapevine species. Here we report an Illumina short-read 369X coverage, draft de novo heterozygous genome sequence ofV. ripariaMichx. ‘Manitoba 37’ with the size of ~495 Mb for 69,616 scaffolds and a N50 length of 518,740 bp. Using RNAseq data, 40,019 coding sequences were predicted and annotated. Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models found 96% of the complete BUSCOs in this assembly. The assembly continuity and completeness were further validated usingV. ripariaESTs, BACs, and three de novo transcriptome assemblies of three differentV. ripariagenotypes resulting in >98% of respective sequences/transcripts mapping with this assembly. Alignment of theV. ripariaassembly and predicted CDS with the latestV. vinifera‘PN40024’ CDS and genome assembly showed 99% CDS alignment and a high degree of synteny. An analysis of plant transcription factors indicates a high degree of homology with theV. viniferatranscription factors. QTL mapping toV. riparia‘Manitoba 37’ andV. viniferaPN40024 has identified genetic relationships to phenotypic variation between species. This assembly provides reference sequences, gene models for marker development and understandingV. riparia’s genetic contributions in grape breeding and research.