To overcome some of these challenges posed by ND climate, the utilization of native wild Vitis-derived varieties is the best possible option available. Despite advantageous environmental tolerances of native wild Vitis spp. derived crosses, their acid and sugar concentrations often deviate from expectations set for V. vinifera. Identifying the genetic determinants of titratable acidity (TA), pH, and total soluble solids (TSS/°Brix) in interspecific hybrid populations can help improve new hybrid cultivars. For this purpose, an incomplete diallel mapping population with substantial riparia and other wild Vitis spp. in its background was used to perform association studies. The population is genotyped with single nucleotide polymorphism (SNP) markers and phenotyped over two years. Genome wide association analysis (GWAS) identified a significant association on chromosomes 6 and 16 for all three traits in both years. Candidate gene identification under the significant region revealed multiple glucose, fructose, and amino acid metabolism genes.