The molecular marker (SSR) has been used to investigate the markers associated with the agronomic traits including days to 50% flowering, tube ring time, days to maturity, plant height, the number of main stems per plant, the number of tubers per plant, dry matter content, main stem diameter, a single tuber weight, average single tuber weight, and the total yield in potato genotypes. Ten primers used in 16 potato genotypes were investigated and principal component analysis and cluster analysis were used to determine genetic distance and genotype classification. A significant difference was found between all cultivars, indicating high genetic diversity for the traits under study, except for the diameter of stem trait. Yield showed a significant positive correlation with the number of tubers per plant, weight of tubers per plant, single tuber weight, and the number of main stems per plant. Special values resulted from components of 1-5 were higher than 1 in principal component analysis and totally justifying 76.70% of all variables variances. Molecular diversity of cultivars was measured using parameters of polymorphic information, the number of effective alleles, and Shannon index and the average of 39.03 SSR bands was achieved among which 9.41 bands were polymorphic. The average number of polymorphic bands varied for each primer from 1.56 to 2.12. Maximum and minimum polymorphic bands belonged to the HVM70 primer with 2.12 and the Bmacoo40 primer with 1.56, respectively. Also, the mean maximum band (4.4) and minimum band (3.1) belonged to Agra and Deyta cultivars, respectively. The morphologic data did not conform to the molecular data indicating that SSR marker had no genetic relationship with positions controlling the measured morphologic traits. Since the SSR markers were located in non-coding area of genome, no relationship between classifications of molecular markers and morphologic data was unexpected. Manuscript profile