Abstract The study of the recent colonization of a symbiont and its interaction with host communities in new locations is an opportunity to understand how they interact. The use of isotopic ratios in trophic ecology can provide measurements of a species’ isotopic niche, as well as knowledge about how the isotopic niches between symbiont and host species overlap. Stable isotope measurements were used to assess the sources of carbon assimilated by the host species (the bivalves Mytilus galloprovincialis and Scrobicularia plana) and their associated symbiont pea crab Afropinnotheres monodi, which occurs within these bivalves’ mantle cavities. The mixing model estimates suggest that all of them assimilate carbon from similar sources, particularly from pseudofaeces and particulate organic matter in this symbiotic system based on filter feeding. The symbiotic species occupy comparable trophic levels and its association seems to be commensal or parasitic depending on the duration of such association. The pea crab A. monodi reflects a sex-specific diet, where males are more generalist than the soft females because the latter’s habitat is restricted to the host bivalve. The high isotopic overlap between soft females and M. galloprovincialis may reflect a good commensal relationship with the host.