The rising claim for more environmental friendly and healthy agriculture is a strong incentive to find alternative strategies to replace the use of mineral fertilizer and pesticide. Arbuscular mycorrhizal fungi (AMF), a main component of soil microbiota, represent a promising tool as providers of key ecological services. The present work represented one of the first attempts to study, under a morphological and molecular point of view, the AMF communities associated to some strategic crops in Vietnam. The findings about the AMF morphotypes dominant in different crop systems could be a starting point for the development of well performing and adapted inocula suitable for the application in field.