Mycorrhizal fungi serve as biofertilizers, reduce plant stress, and can increase plant productivity. Since the potato originated from the highlands of Peru and Bolivia, a goal of this research was to utilize indigenous Peruvian mycorrhizal populations to enhance crop productivity in a subsistence production site. The field study was also conducted to test the effectiveness of the flavonoid, formononetin, to stimulate native mycorrhizal activity and subsequent yield of six Andean potato (Solanum tuberosum L.) cultivars. The subsistence site was located at an altitude of 3900 m (61 kPa) in San Jose de Aymara (Department of Huancavelica), in the central highlands of Peru. This is approaching the highest altitude in the world that potatoes are grown. The site had a sandy-loam soil with pH 3.6, low phosphorus (P) availability and high aluminum (Al). Tubers were planted in November 1999, and grown during the rainy season. Minimal organic fertilizer was applied and the potato crop received no supplementary irrigation. Formononetin was applied as a soil drench when shoots from tubers began to emerge. At the end of the 6.5 month study, formononetin increased either potato tuber dry mass and/or Nos. 1 and 2 grade tubers in three of the six cultivars. Soil sporulation of indigenous mycorrhizae was increased more than three-fold by formononetin. There were differences in total mycorrhizal colonization among the six cultivars. The predominant arbuscular mycorrhiza genera at the site were Gigaspora, Glomus and Scutellosporas. © 2005 Elsevier B.V. All rights reserved.