AbstractAerobic methanotrophic bacteria are pivotal in the global carbon cycle by converting methane into biomass and inorganic carbon species. Light rare earth elements (light‐REE; La, Ce) are part of the metalloenzymes mediating the biochemical processes in methanotrophs. However, the partitioning of trace metals and REE in chemosymbiotic megafauna with methanotrophic endosymbionts remains largely unknown. Here we determine stable isotope compositions (δ13C, δ15N) of soft tissues (gill, mantle, foot) as well as trace metal and REE contents of soft tissues and shells of chemosymbiotic bivalves dwelling at methane seeps (Site F and Haima seeps) of the South China Sea. Isotopic compositions of soft tissues are found to reflect the mode of chemosymbiosis (i.e., methanotrophy vs. thiotrophy). Particularly gill tissues of bivalves with methanotrophic endosymbionts display marked light‐REE and trace metal enrichments, which is interpreted to reflect the enzymatic activity of endosymbionts. Additionally, correlations between light‐REE and copper (Cu), zinc (Zn), and molybdenum (Mo) contents in soft tissues of chemosymbiotic mussels are ascribed to the uptake of these elements by the methanotrophic symbionts. An observed higher trace metal content in the tissue of the semi‐infaunal and infaunal bivalves with thiotrophic endosymbionts is believed to reflect the uptake of metals associated with sulfide particles. This study documents diagnostic enrichment of trace metals and light‐REE in the soft tissues of bivalves with chemotrophic endosymbionts and provides new constraints for future identification of chemosymbiosis at ancient seeps.