The current investigation was performed to evaluate the performance and DNA molecular analysis of three grape cultivars under the New Valley governorate, Egypt conditions. Most of the evaluated traits significantly varied among the cultivars. Superior cultivar had the best performance in cluster trait (weight, length and width), berries trait (number per cluster and 100 berries weight) and the total yield per vine. On the other hand, Flame cultivar overtopped in some quality traits (Total Soluble Solids, reducing and total reducing sugars). Molecular analysis was performed by using start codon targeted (SCoT) and inter-simple sequence repeats (ISSR) markers. The detected polymorphism was 68.38% and 41.84%, respectively. The polymorphism information content (PIC) for SCoT and ISSR markers was 0.29 and 0.19, respectively. Thus, SCoT marker was more informative. In contrast, the obtained dendrogram by ISSR showed a better clustering pattern than the SCoT marker.