The hard clam is an economically important species of marine bivalves, however, for the past few years, the tremendous economics losses in clam culture caused by management of aquaculture、global warming and pathogens. Vibrio is a serious problem that restrics the culture industry. Because of probiotics could be use to promote growth, improve water quality, reduce environmental pathogens, and enhance immunity of cultured species, we use the Bacillus pumilus D5 and its mutants to explore those items. Between six months experiments, hard clams treated with B. pumilus D5 exhibited higher growth than B. pumilus NG25 and controls, levels concentration of ammonia and hydrogen sulfide of the treated hard clams were significantly decreased, compared to the controls. Six months after the start of experiments, hard clams were challenged with V. alginolyticus and V. vulnificus, statistical analysis revealed significant difference in hard clams survival between probiotic and control groups. Cumulative mortality of the control group was 60%, whereas cumulative mortality of the hard clams that had been given probiotics was 30% with B. pumilus D5 and 20% with B. pumilus NG25. Subseuently, real-time PCR was employed to determine the mRNA levels of C type lectin (Mm-Lec1). In the bacteria exposure test, the expression of C type lectin genes was only up-regulated in the B. pumilus NG25 and B. pumilus D5 compared to the control groups and the mRNA expression level was highest at 72h, C type lectin play a role in defensing against vibrios invasion in hard clams. In this sense, B. pumilus strains is an ideal multifunctional probiotic bacterium, with the capacity to solve problems and also to increase aquaculture profitability.