The arbuscular mycorrhizal fungi (AMF) are a key, integral component of the stability, sustainability and functioning of ecosystems. In this study, we characterised the AMF biodiversity in a native vegetation soil and in a soil cultivated with Jatropha curcas or Ricinus communis, in a tropical system in Guantanamo (Cuba), in order to verify if a change of land use to biofuel plant production had any effect on the AMF communities.