Using a potato association panel consisting of 34 European cultivars, which had been ranked for drought tolerance based on the drought tolerance index DRYM, SSR markers related to drought tolerance could be identified. Candidate genes for the SSR marker development were selected from literature references and transcript markers from a previous project (TROST). In total, 75 polymorphic SSR markers were obtained, five of them were associated with drought tolerance. These allowed a first selection of drought stress sensitive cultivars in the association panel. However, a UPGMA dendrogram based on the 75 SSR markers did not show a grouping into drought-sensitive and -tolerant cultivars. The new SSR markers, 61 additional published, linkage group specific SSR primer pairs as well as markers from 47 AFLP primer pairs were used to develop genetic maps for all 12 linkage groups in two segregating F1 potato populations, each consisting of > 250 clones. Based on these genetic maps and the provided yield data (starch yield and content, fresh tuber weight), selected transcript and metabolite data as well as data for the drought tolerance index DRYM, QTL analysis could be performed. Numerous QTL could be generated and regions relevant for drought tolerance were identified. A connection between yield QTL and enzymes of the carbohydrate metabolism was also determined. Phytohormones such as ethylene also seem to play an important role. Linkage groups 2 and 12 will be interesting for further drought tolerance investigations in potato, even though genes for this complex trait seem to be present on all 12 linkage groups.