Fifty-one wild potato species were characterized for resistance to late blight in greenhouse experiments. Species showing promising levels of resistance were tested under field conditions. Most of the accessions showed ≥ 50% susceptible individuals when tested under greenhouse conditions. The resistance of 21 species observed under greenhouse conditions was confirmed under field conditions. Population samples of two promising wild species (S. raphanifolium and S. megistacrolobum) and a QTL mapping population derived from S. berthaultii were characterized molecularly for presence of defense gene markers, toward understanding the molecular genetic basis and environmental stability of quantitative resistance. Markers originated from PAL, chalcone isomerase, cytochrome P-450, osmotin and other genes were found to be associated with quantitative resistance and/or quantitative trait loci (QTL) in the new diploid germplasm. Unique gene marker associations with resistance in wild species, with respect to advanced breeding material, suggest that the new germplasm can contribute to broadening the genetic base of resistance.