In order to investigate temporal variation in the arbuscular mycorrhizal (AM) fungal community in a tropical forest in the Republic of Panama, seedlings of the canopy emergent Tetragastris panamensis were sampled three times over a period of 3 years. We used AM-specific primers to amplify and clone partial small subunit ribosomal RNA gene sequences. Over 550 clones were classified into 18 AM fungal types. As the seedlings matured, the fungal diversity decreased and there was a significant shift so that previously rare types replaced formerly dominant fungal types. Further, seedlings of different ages sampled at the same time point were colonised by significantly different fungal populations. Our results indicate that both time and host age may influence the mycorrhizal population.