Methane is an important greenhouse gas whose emissions into the oceans and atmosphere are regulated by relatively unconstrained anaerobic and aerobic microbial processes. The aerobic pathway for methane oxidation is thought to be largely dependent upon the use of rare earth elements (REE), but to date the effects of this process on their abundances in bacteria or in organisms living in symbiosis with methanotrophs remain to be evaluated. Here we show that deep sea chemosynthetic mussels prospering at methane seeps display distinctive lanthanum enrichments linked to the enzymatic activities of their symbionts. These results demonstrate that methanotrophy is able to fractionate efficiently REE distributions in organisms and possibly in the environment. Lanthanum anomalies recorded in ancient sediments are potential chemical fossils that could be used in the geological record for tracking early evidence of microbial life.