A simple biochemical approach for demonstrating the presence of symbionts in deep‐sea bivalves and for discriminating between thiotrophic and methylotrophic symbioses is described. Correspondence analysis (CA) of the free amino compound composition of nine bivalve species living in hydrothermal vents and cold seeps successfully discriminates symbiotic species from nonsymbiotic ones, and sulfur‐oxidizing symbiont from methylotrophic symbionts. CA was also used to infer the metabolism of Bathymodiolus azoricus , B. boomerang , and two new species of Mytilid and Vesicomyid from the Barbados. These results were consistent with the evidence obtained by ultrastructural observations of the gills and enzymatic studies, and show that CA of amino acid profiles might be a useful tool to determine the type of endosymbionts present in deep‐sea bivalves. Among all the free amino acids, thiotaurine appears as the main discriminating one and is proposed as a biomarker of sulfide‐based endosymbiosis in deep‐sea bivalves from hydrothermal vents and cold seeps.