Mutualists have been suggested to play an important role in the assembly of many plant and animal communities, but it is not clear how this depends on environmental factors. Do, for instance, natural disturbances increase or decrease the role of mutualism? We focused on entire guilds of mutualists, studying seed-dispersing ants and ant-dispersed plants along gradients of inundation disturbances. We first studied how abundance and richness of the mutualists, relative to non-mutualists, change along 35 small-scale gradients of inundation disturbances. We found that at disturbed sites, mutualistic plant species, those that reproduce by seeds dispersed by ants, increased in abundance and in consequences in richness, relative to other herbaceous plants. In contrast, we found that among the epigeic arthropods the abundance of mutualists declined, even more so than other arthropods. Correspondingly, distributions of plant and animal mutualists became increasingly discordant at disturbed sites: most plant mutualists were spatially separated from most animal mutualists. We finally found that high abundances of plant mutualists did not translate into a high nutrition service rendered to ants: at disturbed sites, many of the plants of ant-dispersed species did not produce seeds, which coincided with a decline in seed dispersal by ants and a changing searching behavior of the ants. Overall, the small-scale natural disturbances we studied were correlated to a major change in the assembly of mutualist guilds. However, the correlation was often opposite between interacting plant and animal mutualist guilds and may thus reduce the potential interaction between them.