Microcystins (MCs) are a kind of cyanobacterial toxins produced by cyanobacterial bloom. They can affect the growth and reproduction of a variety of aquatic organisms, such as shrimp. In this study, the expression profiles of three antimicrobial peptide genes (Penaeidin 3, Crustin and ALF) in Litopenaeus vannamei were detected via real-time fluorescent quantitative PCR (qRT-PCR) method post MC-LR injection. The results show that MCs can significantly affect the expression of Penaeidin 3 and ALF but cannot affect that of Crustin. In order to understand the impact of MC-LR on the response of the three peptides to bacteria, Vibrio anguillarum was injected into the shrimps after MC-LR injection. The relative expressions of three antimicrobial peptide genes were all down-regulated in the early stage and up-regulated after 4 h post Vibrio anguillarum challenge. Expressions of three genes in MC-LR injected group were all down-regulated compared with the control group. The results suggest that MC-LR could affect the expressions of antimicrobial peptide genes in unkown ways and impact the shrimp immune system.