Antimicrobial peptides (AMPs) are the first line of defense of invertebrates against invading pathogens. Defensins, unique AMPs, have a cysteine-stabilized α-helix and β-sheet (CSαβ) motif. In invertebrates, defensins have been reported in arthropods and mussels. Recently, six defensins were identified from Hyriopsis cumingii for the first time, and were designated as HcDef1, HcDef2, HcDef3, HcDef4, HcDef5, and HcDef6. HcDef1 and HcDef2 encode a protein containing 61 and 60 amino acids, respectively. HcDef3, HcDef4, and HcDef6 have 65 amino acids each. HcDef5 is longer than the other five defensins, comprising 83 amino acids. HcDef3 and HcDef4 have three pairs of disulfide bonds. HcDef1, HcDef5, and HcDef6 are exceptions; each has four pairs of disulfide bonds. Evolutionary analysis revealed that only purifying selection and no positive selection could be detected in defensin genes; purifying selection might be the major evolutionary driving force in the evolution of defensin genes. The present study reveals for the first time that the defensins from H. cumingii are diverse and phylogenetic analysis showed that these 6 defensins from H. cumingii were clustered into one group. Reverse transcriptase polymerase chain reaction (RT-PCR) analysis showed that HcDef1–HcDef4 could be detected in the hepatopancreas and gills whereas HcDef5–HcDef6 could only be detected in gills. In addition, the expression levels of HcDef2, HcDef3, and HcDef5 in H. cumingii with pearls were higher than that in H. cumingii without pearls. Quantitative RT-PCR analysis showed that HcDef1, HcDef2, HcDef3, and HcDef5 were downregulated by Vibrio anguillarum challenge whereas HcDef4 and HcDef6 were upregulated under Vibrio challenge. Our results suggest the roles of defensins in the innate immunity of H. cumingii.