This research was carried out to know the species composition of the Arbuscular Micorrhizal Fungi (AMF) communities native to two contrasting soils, and to establish the development and stability of aggregates in those soils contained in pots, as substrates for corn plants in the greenhouse. These soils were inoculated with allochthonous AMF. The experiment had three factors: Soil (S with two levels [S1 and S2]); AMF (A with three levels: without application [A0], with application of Claroideoglomus claroideum [A1] and with application of a consortium [A2]) and Fertilization (f with two levels (without fertilization [f0] and with fertilization [f1]); which generated 12 treatments, each with five replicates (60 experimental units [EU]); the EU consisted of a pot with a plant of corn; with a completely random distribution. The results showed that the Typic Ustifluvent presented nine species of native AMF, while the Typic Dystrustert had only three species. The native AMF in each soil influenced the activity of the allochthonous AMF, with differences being found in the stability of the macro-sized aggregates (0.5 to 2.0 mm) of each soil when they did not receive fertilization