Marine zooplankton release chemical cues, which trigger defenses in unicellular phytoplankton, such as increased toxin production and changes of colony sizes. Here, we identify the structure of two novel alarm cues belonging to the group of copepodamides. Similar to the known copepodamides, one of the compounds described is shown to trigger both amnesic and paralytic shellfish toxin production and chain length shortening in Skeletonema marinoi. In addition, we report the putative structures of another 21 copepodamides, which constitute 28% of the total copepodamides extractable from whole animals, suggesting that the copepodamide concentrations have been underestimated in earlier studies. We introduce a structure‐based nomenclature to handle the increasing number of copepodamides. Analysis of 12 copepod species showed that marine calanoid and freshwater cyclopoid copepods contain copepodamides. The only harpacticoid included in the analysis, Tigriopus californicus, did not appear to produce detectable amounts of copepodamides. Feeding experiments revealed that copepodamide compositions depend on both diet and species‐specific properties. Copepodamides induce both morphological and biochemical defensive traits in phytoplankton and may drive large‐scale trait–mediated effects in marine food webs. The more comprehensive list of copepodamides reported here makes it possible to explore the role of the copepodamide signaling system in the pelagic ecosystem in greater detail.