Colonisation of decaying leaves fallen from mangrove trees by bacteria and fungi is thought to play an important role at the base of food webs in most tropical estuaries. Compound-specific isotope analysis of amino acids (CSIA-AA) has enabled the previously difficult methodological task of measuring plant, bacterial and fungal energy flows to food webs. Here, we assessed the biosynthetic origins of amino acids at the base of a mangrove food web using the CSIA-AA approach. Trophic positions of the 2 most common mangrove fauna—fiddler crabs and sesarmid crabs—estimated from nitrogen isotopes in phenylalanine and glutamic acid approached 2, suggesting that these species are herbivores rather than microbivores. Consistent with this finding, carbon isotope fingerprints in AAs did not support the importance of essential AAs derived from fungi and bacteria but rather suggested the importance of those originating from plants, especially microalgae. These results suggest that (1) microbial mineralization of decaying leaves supports the production of more easily assimilated microalgae and (2) bacteria and fungi, as intermediates, also routinely incorporate plant-derived AAs into their biomass.