In the present investigation, 17 accessions of Vitis sp. were characterized based on morphological traits and microsatellite markers at ICAR-National Research Center for Grapes, Manjri Farm, Pune during the year 2014–15. Total 21 phenological characters were considered for morphological characterization. Among these, all quantitative traits such as: bunch weight, bunch length, pedicel length, berry length, berry diameter, berry weight, seed weight, titrable acidity, pH and total soluble solids (TSS) showed significant differences among varieties. Red Globe scored highest in terms of yield related parameters such as bunch weight, berry length, berry diameter and 10-berry weight. The molecular data collected from five microsatellite markers produced total 25 DNA fragments. Highest polymorphism was shown by the microsatellite marker VVMD 7 with polymorhic information content (PIC) value 0.80 followed by the VrZag 79 (PIC value: 0.71). Highest allelic diversity (0.82) was observed in VVMD 7. Significant differences were recorded among the accessions with respect to individual microsatellite marker.