Potato is an important non-cereal staple crop serving as a source of food for the large number of worlds population. Genome-wide association study (GWAS) analysis has become a useful tool to uncover the genetic basis of important plant traits by revealing significant association with trait of interest. Present study aimed to explore the phenotypic diversity and to identify the genetic basis associated with important floral traits. A total of 237 tetraploid potato genotypes were used as plant material and field experiments were conducted according to augmented block design for two consecutive years (2016, 2017). Analysis of variance for the studied floral traits reflected highly significant genotypic effects. Mean data for both years resulted significant variation for pistil length (5.53 to 9.92 mm), stamen length (6.04 to 9.26 mm), and pistil length above stamen (1.31 to 4.47 mm). Pearsons correlation analysis reflected highly significant and positive correlation of pistil length with stamen length (r=0.42) and pistil length above stamen (r=0.28). Principal component analysis was performed and the first two PCs were considered that accounted a total of 81.2% variation. Constellation plot divided the studied potato panel into two main populations on the basis of stamen and pistil length. A total of 12,720SNP markers were used for the marker-trait association and a total of 15 markers were found significantly associated with studied traits across both years. Identifying same markers across both years helped in the validation of the obtained marker-trait associations. The identified significant markers reflected some of the putative candidate genes that might be beneficial in potato breeding programs. Up to the best of our knowledge, this is first study identifying the genetic basis of important floral traits and might be helpful to the scientific community interested in potato marker assisted breeding in these traits.