A new peptide, APETx1, which specifically inhibits human ether-a-go-go-related gene (HERG) channels, was purified from venom of the sea anemone Anthopleura elegantissima. APETx1 is a 42-amino acid peptide cross-linked by three disulfide bridges and shares 54% homology with BDS-I, another sea anemone K+ channel inhibitor. Although they differ in their specific targets, circular dichroism spectra and molecular modeling indicate that APETx1 and BDS-I have a common molecular scaffold and belong to the same structural family of K+ channel blocking peptides. APETx1 inhibits HERG currents in a heterologous system with an IC50 value of 34 nM by modifying the voltage dependence of the channel gating. Central injections in mice failed to induce any neurotoxic symptoms. APETx1, which has no sequence homologies with scorpion toxins acting on HERG, defines a new structural group of HERG gating modifiers isolated from a sea anemone.