Monoterpenoid metabolism and aroma compounds are influenced by genetic characteristics. Linalool, α-terpineol, nerol, and geraniol are primary monoterpenoids that have previously been studied in grape (Vitis vinifera) berries. Previous studies were restricted by the lack of relevant studies investigating population structure and the regulatory mechanism underlying monoterpenoid synthesis. In this study, a total of 1133 alleles were amplified, with each locus having on average 6.06 alleles. We also assessed the genetic variability among the genotypes based on 187 microsatellite primer pairs amplified in 96 grape genotypes. The results of the phylogenetic tree analysis showed that the grapevine accessions grouped into five genetic clusters that largely coincided with the recognized species classification and the result of principal coordinates analysis (PCoA). The molecular characterization of these accessions provides insight into genetic diversity, population structure, and linkage disequilibrium (LD) in grapevines. A total of 51 quantitative trait loci (QTLs) were detected that were significantly associated with linalool, α-terpineol, nerol, and geraniol. We found that Deoxyxylulose phosphate synthase (DXS) was located in the region UDV060 on linkage group (LG) 5, whereas Farnesyl diphosphate synthase (FPPS) and Hydroxymethylbutenyl diphosphate reductase (HDR) were located in the VLG19-I-1 and VLG3-A-1 regions, respectively. These novel QTLs will potentially assist in the screening of aroma compounds in grapevines.