Nymphonella tapetis (Pycnogonida, Ascorhynchidae) is an endoparasitic sea spider affecting bivalves. Recently, sea spiders have been found on a massive scale in the commercially important Manila clams (Veneridae, Ruditapes philippinarum) in Japan (Tokyo Bay). Simultaneously, mass mortality has occurred in this area. Local fishers assumed that this mass mortality was caused by the parasitic sea spider, despite the effect of the parasite and parasite intensity on the host being unknown. To evaluate the susceptibility of the Manila clam to sea spider infestation and the impact on mortality levels, we established six treatments at different infection intensities (density of newly hatched larvae of sea spiders) over a 6-month long laboratory experiment. We monitored mortality and three susceptibility indices (clearance rate, sand-burrowing speed and adductor muscle strength) under sufficient food conditions. Parasitization by sea spider affected clearance rate and sand-burrowing speed. The pattern of parasitic intensity effects on survival of Manila clam hosts was shown to be dependent on the levels of parasite numbers, i.e. clams with lower parasitic levels (total of <200 hatching larvae of sea spider given to a host) have a higher survival rate, and high mortality of host clams was shown in excessively higher parasitic densities (400–4000 individuals). Such pattern of parasitic effects on host survival might be one of the causes of mass mortality of Manila clams occurring in the field.