Noncommercial varieties of potatoes (Solanum tuberosum L.) harbor genetic potential for improvements of disease resistance and abiotic stress tolerance in commercial potato cultivars; however, introducing traits from noncommercial varieties to breeding stock can be extremely labor intensive. Molecular genetic markers closely associated with a trait can be used to decrease the time spent phenotyping varieties. Here we review genetic markers that have been used for marker-assisted selection (MAS) in potato. Most MAS markers have been used to detect disease resistance genes, and our review focuses on those markers. Complex traits such as cold, drought and viral tolerance can be studied by comparing expressed genes; next-generation sequencing technologies will help in the discovery of trait-specific molecular markers. This review aids in summarizing the potential of these molecular tools when breeding for complex traits in potato.