The world cultivated potatoes have a narrow genetic base due to their development from a limited germplasm originated in South America. The ability to quickly and accurately identify genetic relationships among potato ( Solanum tuberosum L.) varieties developed in different regions is important for potato breedingprograms, seed and commercial potato growers and marketing.Also the health aspects of vegetables containing high anthocyanin has increased the consumption of colored potatoes rich in anthocyanin in recent years. Anthocyanin’s in blue and purple potatoes are derived from delphinidin, while in the red ones they are resulted from pelargonidin. Three genes, D , P and R interact for production of delphinidin and pelargonidin within the anthocyanin biosynthesis pathway that eventually results in colored potato flesh. Studying genic and allelic relations among these three major genes provides a better understanding of anthocyanin biosynthesis pathway in potato.To understand genetic relationships,this study rendered 25 useful SSRs and EST-SSRs markers that were located in pre-existing genetic mapsand fingerprinted a set of 48 potato cultivars from America, Iran and Europe. The number of alleles per locus ranged from 3 to 12 with an average of 6.22 per locus. kimura 2 parameterssimilarity coefficients were estimated from the molecular data and Minimum Evolution cluster analysis was performed. Markersused successfully revealed diversity between different cultivars due to their morphological and physiological characteristics.To detect the three anthocyanin key genes of D,P and R specific primers were used on 17 potato genotypes of varying tuber color and their restriction fragment patterns compared . Althought there is some differences between the sequences of each of the three genes in white and colored potatoes, but the results showed that D is an important regulatory gene for both P and R genes and the dominant allele D is required for their expression and anthocyanin production in the potato tuber. The key role of D locus in regulating structural genes in anthocyanin biosynthesis pathway motivated the transformation of white coloredIstanbuli cultivarwith this gene. Transformation upregulated anthocyanin biosynthesis structural genes and increased anthocyanin content of transformed Istanbuli cultivar when compared to untransformed counterpart.You need a concluding sentence here as well. Key words: Potato ( Solanum tuberosom , Anthocyanins, D , P and R loci, potato transformation.