Black dot and silver scurf are potato blemish diseases that reduce tuber quality. Although they had been considered of minor importance in the past, the commercialization of washed pre-packed potato tubers has led to an increase awareness of these diseases in the past 20 years. In this thesis, black dot and silver scurf are studied at the agronomic, cytologic and metabolomic levels. Field trials revealed the biotic and abiotic factors that affect the development of both diseases. Microscopy and metabolomics analysis of different potato cultivars exposed structural and biochemical factors of resistance to both diseases. Finally, a chemical characterization of plant extracts with potential as post-harvest control treatments was carried out. Overall, this thesis gives new insights in the epidemiology, host resistance and post-harvest control of black dot and silver scurf in potatoes, and control measures against both diseases are suggested to elaborate an integrated pest management.