The species V. vinifera L., is the main species used today for wine. It is a diverse species at the morphological level. In order to estimate the diversity of the nuclear and chloroplastic genomes, molecular markers have been developed. These markers can also be used to authenticate species and cultivars from a range of grape tissues. Today, the most popular markers in use by the grape community are the microsatellites. However, identification of clones from diverse cultivar backgrounds requires additional methodologies and remains difficult. Microsatellite markers have been used for the authentication of grape varieties from experimental wines but their application has not yet been possible for commercial wines. This chapter reviews the methodologies for analyzing DNA from grapes and wines and presents some of the limitations and challenges that remain in using this technology for authentication of grape species, cultivars, and clones from a range of grape tissues.