In coastal areas that are affected by continuous, seasonal or occasional pollution sources, bivalves accumulate biological contaminants such as pathogenic bacteria. We investigated the effect of natural seawater relaying and electrolyzed seawater depuration on the bacteriological quality of artificially contaminated oysters Crassostrea gigas and short-necked clams Ruditapes philippinarum to suggest an alternative method of shellfish sanitation control.When artificially contaminated oysters and short-necked clams (fecal coliform level 1,700 MPN/100 g) were relayed into a sea area of safe bacteriological water quality, the fecal coliform level dropped to below 110 MPN/100 g after 1 day. The bacteriological quality of oysters and short-necked clams that are contaminated at a fecal coliform level of 1,700 MPN/100 g could be improved, and become appropriate for raw consumption by a single day relay under proper environmental conditions. When artificially contaminated oysters (fecal coliform level 330 MPN/100 g) were depurated with electrolyzed seawater, 94% of fecal coliform was eliminated after 12 h and fecal coliform was undetectable after 24 h. After 24 h depuration with electrolyzed seawater, the fecal coliform level of short-necked clams with initial fecal coliform of 2,400 MPN/100 g was below 20 MPN/100 g. However, the fecal coliform level of short-necked clams with initial fecal coliform of 17,000 MPN/100 g was relatively high, at 790 MPN/100 g, even after 24 h of depuration with electrolyzed seawater, because of the repeated cycle of excretion and accumulation of fecal coliform in shellfish tissue under the closed depuration environment. Such natural seawater relaying and electrolyzed seawater depuration can be restrictively applied to improve or secure the bacteriological quality of oysters and short-necked clams in accordance with safety levels for bivalves for raw consumption.