We explored the distribution of Cardicola chaetodontis in chaetodontid fishes from the Great Barrier Reef. We found just four infections of adult worms in 238 individuals of 26 chaetodontid species. By contrast, eggs were present in hearts of 75 fishes (31·5%) and 19 of 26 chaetodontid species (all Chaetodon species). In 10 cases eggs contained moving miracidia; all the others were dead and degenerating. Eggs were sought in the gills of 51 individual fish. There were 17 cases of eggs being present in gills while present in the heart, but also 13 cases where eggs were absent from gills but present in the heart, suggesting that eggs remain longer in heart tissue than in gills. ITS2 rDNA sequences from two adult worms and eggs extracted from gills of five fishes (all different species) were identical to previously reported sequences of C. chaetodontis except for a single base-pair difference in two samples. We conclude that aporocotylid eggs trapped in fish heart tissues may inform understanding of the distributions and host ranges of aporocotylids, especially where adult prevalence is low. The low host-specificity of C. chaetodontis contrasts with higher specificity of trematodes of chaetodontids that have trophic transmission.