Sequence data were combined with morphological analyses to identify two lepocreadiid trematode species from jellyfishes and fishes. Three species of jellyfish were captured within Port Phillip Bay, Australia, and three species of fish that feed on jellyfish were obtained from Moreton Bay (Queensland) and Port Phillip Bay and Portland (Victoria). The digeneans were distributed throughout most parts of the jellyfish. Opechona cf. kahawai Bray & Cribb, 2003 parasitized the scyphozoan jellyfish Aequorea eurodina and the scombrid fish Scomber australasicus. Cephalolepidapedon warehou Bray & Cribb, 2003 parasitized the scyphozoans Pseudorhiza haeckeli and Cyanea annaskala, and the centrolophid fishes Seriolella brama and Seriolella punctata. Intensities ranged from four to 96 in the jellyfish, and one to 30 in the fish. For both trematode species, internal transcribed spacer 2 of ribosomal DNA sequences from mature adults in the fishes matched those from metacercariae from the jellyfish. This is the first record of larval stages of C. warehou and O. cf. kahawai, and the first use of DNA sequencing to identify digenean trematode metacercariae from jellyfish. Three new host records are reported for C. warehou and two for O. cf. kahawai.