This is the first study in Brazil to propose a trophic relationship between Chaetognatha and Cnidaria based on molecular data (COI gene - DNA barcode). Cnidaria COI sequences were detected in tissue samples from two specimens of Flaccisagitta enflata collected in the surroundings of Fernando de Noronha archipelago, Tropical Western Atlantic. The methodology used followed all the requirements for a safe molecular manipulation, making the possibility of contamination unlikely. A search carried in BLAST showed that both sequences provided here presented a combination of highest query coverage and match identity with Nemopilema nomurai (Cnidaria: Scyphozoa), supporting the hypothesis that they belong to a species of jellyfish. Since gelatinous taxa are known to integrate the broad diet of Chaetognatha, it is possible that F. enflata has ingested this type of item, which was not fully digested until the moment of sampling and was not visualized by the transparency method. Thus, the record of Scyphozoa by the COI marker suggests a trophic relationship between the respective taxon and F. enflata. Future studies using the association of markers as well as specific methodologies may constitute a new perspective on how to evaluate the trophic ecology of key zooplankton species, including the abundant F. enflata in the Atlantic ocean.