To determine the synergistic disinfection effect of the combined treatments of sodium hypochlorite (NaClO), irradiation, and vitamin B(1), the bactericidal effects of the treatments on natural microflora of oyster and short-necked clam were investigated. Then, bacteria isolated from the samples were identified by 16S rDNA sequencing. Oyster and short-necked clam were mainly contaminated with Vibrio spp. and Bacillus spp. Total number of aerobic bacteria ranged from 10(2) to 10(4) colony forming units (CFU)/g initially. More than 100 mg/L of NaClO with 1000 mg/L vitamin B(1) and 2 kGy irradiation treatment for oyster and short-necked clam can reduce the total aerobic bacteria to the level of lower than a detection limit (10 CFU/g). Synergistic effects were observed for all combined treatment against natural microflora. The results suggest that a significant synergistic benefit can be achieved by a combination of NaClO-ionizing radiation treatment with the addition of vitamin B(1) to reduce the microbial population contaminated in oyster and short-necked clam.