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Diabetes mellitus is one of the most serious diseases of our century. The drugs used are limited or have serious side effects. The search for new sources of compounds for effective treatment is relevant. Magnificamide, a peptide inhibitor of mammalian α-amylases, isolated from the venom of sea anemone Heteractis magnifica, can be used for the control of postprandial hyperglycemia in diabetes mellitus. Using the RACE approach, seven isoforms of magnificamide were detected in H. magnifica tentacles. The exon–intron structure of magnificamide genes was first established, and intron retention in the mature peptide-encoding region was revealed. Additionally, an α-amylase inhibitory domain was discovered in the mucins of some sea anemones. According to phylogenetics, sea anemones diverge into two groups depending on the presence of β-defensin-like α-amylase inhibitors and/or mucin-inhibitory domains. It is assumed that the intron retention phenomenon leads to additional diversity in the isoforms of inhibitors and allows for its neofunctionalization in sea anemone tentacles. Bioprospecting of sea anemones of the order Actiniaria for β-defensin-like α-amylase inhibitors revealed a diversity of inhibitory sequences that represents a starting point for the design of effective glucose-lowering drugs.