The potential for mycorrhizae to influence the diversity and structuring of plant communities depends on whether their affinities and effects differ across a suite of potential host species. In order to assess this potential for a tropical forest community in Panama, we conducted three reciprocal inoculation experiments using seedlings from six native tree species. Seeds were germinated in sterile soil and then exposed to arbuscular mycorrhizal fungi in current association with naturally infected roots from adults of either the same or different species growing in intact forest. The tree species represent a range of life histories, including early successional pioneers, a persistent understory species, and emergent species, typical of mature forest. Collectively, these experiments show: (i) the seedlings of small-seeded pioneer species were more dependent on mycorrhizal inocula for initial survival and growth; (ii) although mycorrhizal fungi from all inocula were able to colonize the roots of all host species, the inoculum potential (the infectivity of an inoculum of a given concentration) and root colonization varied depending on the identity of the host seedling and the source of the inoculum; and (iii) different mycorrhizal fungal inocula also produced differences in growth depending on the host species. These differences indicate that host–mycorrhizal fungal interactions in tropical forests are characterized by greater complexity than has previously been demonstrated, and suggest that tropical mycorrhizal fungal communities have the potential to differentially influence seedling recruitment among host species and thereby affect community composition.