Technical Abstract: Vitis (Vitaceae) is a taxonomically complicated genus with ca. 60 taxa divided into two subgenera, Vitis and Muscadinia. We used population genetic approaches to gain insights into the genetic diversity, patterns of evolutionary differentiation and to decipher the taxonomic status of some of the controversial taxa within the genus Vitis. The distance- and model-based analyses were used to examine the phylogenetic structure within the genus Vitis using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. The results closely matched the current classification, but some discrepancies in the identity of taxa at the specific and subspecific levels were still evident. The East Asian the North American Vitis exhibited strong divergence and each group showed further differentiation into several subgroups with North American subgroups roughly matching the described series. The model based cluster analysis indicated 14 clusters as optimum to explain the genetic structure within the genus Vitis with most clusters containing a moderate frequency of admixed genotypes suggesting interspecific gene flow within the subgenus Vitis. Hierarchical partitioning of molecular variation indicated that a significant amount of total variation (~74% and ~69% for SSRs and AFLPs, respectively) is accounted for by intraspecific variation as compared to the levels due to genetic differentiation among species within series (~17% and ~20% for SSRs and AFLPs, respectively) and among series within the genus Vitis (~9% and ~10% for SSRs and AFLPs, respectively). Overall, Vitis possesses mild genetic structure characterized by reticulation and incomplete lineage sorting of ancestral polymorphisms.