In order to utilize seaweeds as a natural therapeutic agent in aquatic cultures, it is important to evaluate their antimicrobial activities. We analyzed that of the typical seaweeds of the Zhejiang Coast in order to improve their potential utilization. Six species of seaweeds were collected from the Zhejiang coast—Ulva pertusa, Ulva prolifera, Gloiopeltis furcata, Gracilariopsis lemaneiformis, Sargassum fusiforme and Ishige okamurae—and their ethanolic extracts were tested for antibacterial effects as well as antiviral activity against the white spot syndrome virus (WSSV). The seaweed extracts inhibited bacterial growth in vitro, and increased the immune responsiveness and survival of the crab Scylla paramamosain infected with WSSV in a concentration-dependent manner. U. prolifera, G. lemaneiformis, and S. fusiforme showed the most potent antibacterial activities and most significant enhancement of the innate immunity in healthy crabs. In conclusion, our study showed that the seaweed extracts have therapeutic effects and are a potential natural medicine for aquatic animals.