The family Bacillaceae bacteria, particularly Bacillus communities, are useful and attractive probiotics with desirable features to fulfill the vast demand for aquaculture. In Hainan Island, the coastal aquaculture ponds hold about 1% of the total area in China, whereas the knowledge of Bacillaceae bacterial communities was limited. Herein, the Bacillaceae bacterial communities in the coastal aquaculture ponds of the artificial ponds (lined with high-density polyethylene plastic sheets) and earthen ponds were investigated by the culturable method. The characteristics of culturable Bacillaceae communities in these two types of coastal aquaculture ponds showed a massive difference. All the culturable Bacillaceae bacteria were identified as Bacillus in the artificial ponds, whereas the earthen ponds were dominated by Bacillus followed by Halobacillus. It is worth noting that the artificial ponds with a low Bacillaceae diversity displayed a high Bacillaceae concentration with a better water quality, whereas the earthen ponds with a higher Bacillaceae diversity and concentration displayed a higher risk of Vibrio infection, indicating that the Bacillaceae concentration than its diversity made a greater contribution to water purification and Vibrio control. This work besides providing a promising strategy for healthy coastal aquaculture by balancing the relationship between Bacillaceae concentration and its diversity also will lay a foundation for the development of probiotic Bacillaceae agents for wastewater purification and disease control.