Morphological characteristics of arbuscular mycorrhizal fungi (AMF) were studied in a cross-inoculation assay of potted seedlings of cacao (Theobroma cacao L.) and legume shade tree guaba (Inga edulis Mart.). Roots of both species and undisturbed soil blocks from an agroforestry system in the Costa Rican humid tropics were used as inocula. Paris type arbuscules were more abundant than arum type in T. cacao roots while the two types were equally abundant in I. edulis. Twelve spore morphotypes were identified. Population structure of AMF spores formed in the soil block was different from those formed by either T. cacao or I. edulis roots in heat-treated soil; the populations formed by the two root inocula were quite similar. Same AMF morphospecies colonized both host plants. Thus, these trees may interact via mycelial connections in agroforestry systems.