We describe an emerging pathology, brown muscle disease (BMD), which specifically affects the Manila clam Ruditapes philippinarum in Arcachon Bay (France). BMD induces a transformation of the posterior adductor muscle, which becomes infused by conchiolin and calcified, reducing the ability of clams to bury. The disease affects both types of muscular tissue, with striated muscle becoming affected to a higher degree than smooth muscle. Two indices were created to quantify the symptoms: the Muscle Print Index, used for empty and live shells, and the Final Disease Index, utilized for live clams only. Histological sections were made and observed under light microscopy to examine the muscular damage and to investigate a causal agent. Sections revealed an important inflammatory response with a large invasion of hemocytes into tissues and a heavy necrosis of muscular fibers. Additionally, molecular biology analyses were carried out to search for bacteria and protozoan agents using generic primers. In both histological and molecular assays, bacteria and protozoans were discounted. We monitored 4 sites scattered around the bay over 2 yr. The mean prevalence was < 12% without seasonal variation in 3 sites against 30% and a winter peak in 1 site. The latter site was accurately surveyed and revealed that clams at the sediment surface (abnormal position) were affected 3 times more frequently than buried clams (normal position).