To study the isolation rate and toxin type of Clostridium perfringens in fresh Meretrix meretrix Linnaeus, one hundred gut samples of Meretrix meretrix Linnaeus bought from market were examined bacteriologically for the occurrence of C. perfringens. Isolates were examined by polymerase chain reaction (PCR) for genes encoding the four lethal toxins (α, β, ε and ι) for classification into toxin type and for genes encoding enterotoxin and the novel β2 toxin for further subclassification. The amplified complete α toxin gene was cloned and sequenced and compared with strains isolated from other living environment. Then, alpha toxin gene detected from Meretrix meretrix Linnaeus muscle (C. perfringens positive in gut)was performed for food safety assessing. The results indicated that C. perfringens could be isolated in 71 gut samples (71%) from Meretrix meretrix Linnaeus, 49 strains (69%) were C. perfringens toxin type C (α and β toxin positive), 22 strains (31%) were toxin type A (α toxin positive). In addition, genes encoding for β2 toxin and enterotoxin were found in the both toxin types. These amplified toxin gene fragments were cloned and sequenced and compared with the corresponding genes in GenBank, and the identity exceeded 98%. The homology of complete α toxin gene was 98.64%-99.58％ when compared with strains isolated from other living environment. This is the first report of C. perfringens toxin genes in Meretrix meretrix Linnaeus in general, the origin of this bacterium and its importance to human food poisoning are discussed.