Two marine antimicrobial peptides (AMPs), PC-hepc from large yellow croaker (Pseudosciaena crocea) and scygonadin from mud crab (Scylla serrata), are potently active against specific bacteria and thus they could be used as substitutes for antibiotics in aquaculture. However, how to utilize the AMPs feasibly for marine cultured animals has been so far confused. In our study, a 510 bp of the Scy-hepc sequence was cloned into pMDC85 expression vector, which was then electroporated into Chlorella sp., and thus a transgenic Chlorella, in which the Scy-hepc gene was effectively expressed, was developed. The Scy-hepc fusion protein was successfully expressed in Chlorella sp. and it showed obvious bactericidal activity. In addition, the in vivo efficacy of the transgenic Chlorella was evaluated using Sparus macrocephalus and the hybrid Epinephelus fuscoguttatus (♀) × Epinephelus lanceolatus (♂). Results showed that the survival rate of S. macrocephalus fed with transgenic Chlorella (80 ± 10% after 72 h) was significantly higher than that of fish fed with the same dosage of wild-type Chlorella (33.33 ± 11.55% after 72 h). Similarly, results showed that the survival rate of the hybrid grouper fed with transgenic Chlorella (55 ± 5% after 36 h) was much higher than that of fish fed with the same dosage of wild-type Chlorella (25 ± 5% after 36 h). Therefore, in vitro and in vivo results indicated that the constructed transgenic Chlorella with the marine AMPs Scy-hepc could exert effective protection for fish against the Aeromonas hydrophila infection, providing an encouraging prospect for the expected use of transgenic Chlorella in aquaculture in future.