The nutritional role of endosymbiotic sulfur-oxidizing chemoautotrophic bacteria in animal-bacteria symbioses was investigated using the endosymbiont-containing protobranch clam, Solemya velum, as a general model of animal-bacteria symbioses. Animal-bacteria symbioses are often very difficult to maintain in the laboratory; consequently, it is difficult to carry out physiological experiments on these organisms. As a result, a detailed biochemical characterization of S. velum was undertaken in order to determine the presence of biochemical markers of endosymbiont activity which might be useful in determining the nutritional importance of the endosymbiotic bacteria. Analysis of the stable isotope ratios, lipid, and amino acid compositions of S. velum revealed the presence of strong endosymbiont biomarkers which demonstrate that bacterial endosymbionts serve as the major nutritional source for this bivalve. The endosymbiotic bacteria may provide almost 100% of the host's C and N budgets, and much of the host's lipid and amino acid requirements. Analysis of the stable isotope and lipid composition profiles of two additional animal-bacteria symbioses, Solemya borealis and Inanidrilus leukodermatus, also revealed the presence of biochemical markers of endosymbiont activity, demonstrating the nutritional importance of endosymbiotic bacteria in these species. The biomarker approach is extremely useful in the study of nutrition in animal-bacteria symbioses.