The diversity of arbuscular mycorrhizal fungi (AMF) communities in agricultural systems depends on biotic and abiotic factors as well as on cultural practices. This research aimed to evaluate the diversity of AMF present in an altitudinal transect cultivated with cape gooseberry (Physalis peruviana L.). A set of 13 soil samples from cape gooseberry plantations located in the Colombian Andean mountains in the provinces of Cundinamarca and Boyaca were collected during dry (0-20 mm/month) and rainy (150-330 mm/month) seasons between 1500 and 3000 m a.s.l., in order to establish the relationship between the altitudinal characteristics and AMF diversity. The evaluation of the abundance of spores and species and diversity indexes showed the presence of 46 AMF species in the dry season and 31 in the rainy season. This shows the high diversity of AMF in the tropical Andes with spore abundance between 20 and 120 spores 10 g-1 of soil in the rainy season and between 127 and 1531 spores 10 g-1 of soil in the dry season.