In this article, we show how a disease could bias stable isotope analyzes of trophic networks and propose a strategy in the choice of tissues to be analyzed. In the past few years, a new pathology (brown muscle disease or BMD) affecting the posterior adductor muscle of Ruditapes philippinarum has emerged in Arcachon Bay. BMD induces a necrosis of muscle tissues which become infused by conchiolin and hence calcified. As muscle of mollusks are often used for trophic food webs studies through stable isotopic analyzes, this work investigated the effect of BMD on carbon and nitrogen isotopic ratios of anterior and posterior adductor muscles of clams collected in February and August 2007. Infected clams displayed a lower condition index and a posterior adductor muscle delta C-13 enrichment of 1.2aEuro degrees in February and 0.7aEuro degrees in August. delta N-15 of posterior muscles was however not affected by the disease. Anterior muscle of diseased clams remained healthy and displayed the same isotopic signature as both posterior and anterior muscular tissues of healthy clam. Acidification significantly depleted delta C-13 in posterior muscles of infected clams, suggesting calcification, contrary to anterior muscles of infected clam and to both muscles of healthy clams, where no effect was observed. An X-ray diffractometry analysis confirmed the presence of CaCO3 (aragonite). Trophic food web studies relying on stable isotope ratios should utilize only healthy animals or anterior adductor muscles when expertise in mollusk pathology is lacking.