In this study forty-five table grape Iranian cultivars were assessed by using 42 retrotransposon-microsatellite amplified polymorphism (REMAP) markers also analyzing population structure, linkage disequilibrium and genomic regions associated with most important berry yield and quality traits. The phenotypic results showed the great diversity of the Iranian germplasm and their suitability for genetic and association studies. The studied grape cultivars were divided into three populations. A significant level of LD was observed in 1.22% of the retrotransposon marker pairs (P < 0.01). Mixed linear model procedure revealed that 40 loci had significant association with investigated traits. Finally, 27 markers showed significant association with regions controlling the studied berry yield and quality traits. These REMAP loci identified in this study associated to phenotypic traits may be applied in marker-assisted selection in table grape breeding programs.