Cetaceans (whales, dolphins, and porpoises) are a diverse and widely distributed group of fully aquatic placental marine mammals. Chromosome-level reference genomes are important for evolutionary analyses, demographic histories and conservation efforts of cetaceans. The melon-headed whale (Peponocephala electra) is a small- to medium-sized toothed whale of the oceanic dolphin family (Delphinidae). The melon-headed whale genome will contribute to research on cetacean evolution, adaptations, demographic histories, and conservation in the future.