Phytophthora infestans (Mont.) de Bary causing potato late blight (LB) and potato virus Y (PVY), are serious constraints to cultivated potatoes causing important yield reduction, and phenotyping for resistance is challenging. Breeding operations for vegetatively propagated crops can lead to genotype mislabeling that in turn reduces the genetic gain. Low-density and low-cost molecular marker assessment for phenotype prediction and quality control stands as a viable option for breeding programs. We report here the development of Kompetitive Allele Specific PCR (KASP) markers for LB and PVY resistance, and for quality control assessment, and their routine use in different breeding populations. Two KASP markers for LB resistance and two for PVY Ryadg were validated with an estimated assay power ranging between 0.65 and 0.88. Developed QC KASP markers demonstrated the power of tetraploid calls in discriminating the breeding material, including full sibs and half sibs. The routine implementation of developed markers in a breeding program will allow a better allocation of resources and a precise characterization of the breeding material, leading to an increased genetic gain.