High contents of sucrose (non-reducing sugar), glucose and fructose (reducing sugars) in potato tubers represent an undesirable trait for fry processing because reducing sugars lead to potato darkening and the production of toxic compounds such as acrylamide that reduce consumer’s acceptance and generate risks for human health. Association genetics analysis is a strategy to study the molecular basis of complex traits as tuber sugar contents. Colombia leads the production of diploid genotypes named “Creole potato”, which belong to the cultivated Group Phureja and present outstanding organoleptic and nutritional properties. Currently, there are not Phureja cultivars suitable for chip processing because of high levels of reducing sugars in the tubers. The main purpose of this research is to determine the candidate gene regions influencing sucrose, glucose and fructose contents in Solanum tuberosum Group Phureja. Tubers from 108 accessions of the Colombian Core Collection and four commercial cultivars were sown in pots in Soacha (Cundinamarca, 2850 m above the sea level) for sugar content analyses. The harvest of three plants of each genotype constituted three biological replicates. The sugar contents of Phureja genotypes were quantified through a liquid chromatographic method developed and validated using an AMINEX87H column with sulfuric acid 10 mM as eluent. Sucrose, glucose and fructose genotypic mean values varied from 6.39-29.48 mg/g tuber dried weight (DW), 0.46-28.04 mg/g tuber DW, and 0.29-27.23 mg/g tuber DW, respectively. Association analysis was carried out with 111 SNP markers identified in candidate genes with key function in carbohydrate metabolism. This analysis revealed four SNP markers in the locus InvGE from an apoplastic invertase and one SNP marker in the locus SssI from a soluble starch synthase with significant effect in sugar content variation. These enzymes have not been found expressed in mature tubers, therefore these SNP-trait associations might be indirect resulting from the linkage disequilibrium with causal variants, or direct through a potential novel role of these candidate genes controlling sugar contents in tubers.