Pigmented potato contains massive antioxidants such as anthocyanin and flavonoid, thus they can be used as nutrient and healthy foods. To investigate the genetic background of pigmented potato and provide effective information on parental combination for potato breeding, we used 22 SSR markers for genetic diversity analysis and fingerprint profile of 33 pigmented potato varieties (lines). The results indicated that 95 alleles were amplified from 22 SSR markers, and 82 alleles showed polymorphism. Polymorphism information contents (PIC) of 22 SSR markers ranged from 0.168 7 (STM1053) to 0.991 9 (STI033) with an average of 0.841 1. UPGMA method was used for clustering analysis. With the similarity coefficient of 0.71, all the pigmented potatoes were classified into four cluster groups. A significant diversity was found among four cluster groups. Five SSR markers (STM0031， STM0030, STI014, STM1029, STI001) were used to select construct the molecular fingerprint profile of 33 pigmented potato varieties (lines). The research results were useful to the parental combination during breeding for pigmented potato and rapid identification of pigmented potato germplasm resources.