In this research, antagonistic activity of two Bacillus species isolated from digestive tract of marine fish and culture pond of sea cucumber was studied. The inhibitory activity of Bacillus spp. isolates against some common pathogenic bacteria of fish was assessed using the agar diffusion method. The strain of B. subtilis G024 exhibited antimicrobial activity against Vibrio anguillarum, V. harveyi, V. vulnificus, Streptococcus sp. and Staphylococcus aureus; the isolate of B. amyloliquefaciens N004 inhibited growth in V. anguillarum, V. campbellii, V. vulnificus, V. parahamolyticus, Edwardsiella tarda, Streptococcus sp., B. cereus. Scanning electron microscopy (SEM) investigation of indicator bacteria showed that cell morphologies were strongly affected by the cell-free supernatant of the two Bacillus spp. isolates. It is determined that the culture filtrates contained inhibitors against growth of some pathogenic bacteria with different degrees of inhibition, although none of the culture filtrates could inhibit the growth of V. fluvialis, V. alginolyticus, V. splendidus. Based upon these characteristics, both of the antagonistic Bacillus spp. isolates could be the potential probiotics used in the aquaculture production.