Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide micronutrient malnutrition. In the present study, we report on the identification of single nucleotide polymorphism (SNP) markers associated with folate, an essential micronutrient in the human diet. A high folate diploid clone Fol 1.6 from the wild potato relative Solanum boliviense (PI 597736) was crossed with a low/medium folate diploid S. tuberosum clone USW4self#3. The resulting F1 progeny was intermated to generate an F2 population, and tubers from 94 F2 individuals were harvested for folate analysis and SNP genotyping using a SolCap 12K Potato SNP array. Folate content in the progeny ranged from 304 to 2,952 ng g-1 dry weight. 6,759 high quality SNPs containing 4,174 (62%) polymorphic and 2,585 (38%) monomorphic SNPs were used to investigate marker-trait association. Association analysis was performed using two different approaches: survey SNP-trait association (SSTA) and SNP-trait association (STA). A total of 497 significant SNPs were identified, 489 by SSTA analysis and 43 by STA analysis. Markers identified by SSTA were located on all twelve chromosomes while those identified by STA were confined to chromosomes 2, 4, and 6. Eighteen of the significant SNPs were located within or in close proximity to folate metabolism-related genes. Forty two SNPs were identical between SSTA and STA analyses. These SNPs have potential to be used in marker-assisted selection for breeding high folate potato varieties.