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ABSTRACT Crown‐of‐thorns sea star (CoTS) outbreaks are a main cause of hard coral cover decline across the Indo‐Pacific, posing a major threat to the resilience of coral reefs. However, the drivers underlying CoTS feeding on preferred (e.g.,Acroporaspecies) versus non‐preferred (e.g.,Poritesspecies) are poorly understood. We hypothesised that coral venom may influence CoTS prey preferences. To investigate this hypothesis, we compared the coral venom toxin families across the genomes of preferred (A. digitifera,A. hyacinthus,A. milleporaandA. tenuis) and non‐preferred (P. australiensis,P. compressa,P. luteaandP. rus) prey species of CoTS. We also included one species from each genus inhabiting the Caribbean, where CoTS are absent (A. cervicornisandP. astreoides), to broaden our identification of venom constituents shared within each genus and investigate geographic differences. We collected known cnidarian toxins, and along with the cnidarian Tox‐Prot database, used these to identify putative toxins and investigate their phylogeny. The most abundant toxins across all coral species included neurotoxins (kunitz‐type and SCRiPS) and pore‐forming toxins (actinoporins and MAC‐PFs). We found genera‐specific differences with jellyfish toxins (CFXs) only present inPoritesspecies. Similarly, onlyAcroporaspecies harboured pore‐forming toxins with the aerolysin domain. Two toxin homologues only present in Indo‐Pacific corals (CFX and MAC‐PF homologues) showed evidence of positive selection, suggesting their evolution is shaped by environmental pressures, including exposure to CoTS. These findings provide a foundation for future studies of scleractinian venoms, which have direct applications to assessing reef coral's susceptibility to future CoTS outbreaks and active reef management.