Cardicola Short, 1953 is a genus of the Aporocotylidae Odhner, 1912 (Digenea), with 25 currently recognised species described from 32 species of Perciformes and Mugiliformes fishes around the world, including eight species from the Great Barrier Reef. Here, we describe two new species from this region, namely Cardicola beveridgei n. sp. from the ventricle and atrium of the mangrove jack, Lutjanus argentimaculatus (Forsskål) (Perciformes: Lutjanidae), and Cardicola bullardi n. sp. from the ventricle of the Australian spotted mackerel, Scomberomorus munroi Collette & Russo (Perciformes: Scombridae), from off Lizard Island, Queensland, Australia. These two new species are most easily distinguished from the 25 current members of Cardicola in having the combination of i) a spinous oral sucker, ii) an anteriorly intercaecal ovary, iii) a uterus that extends anteriorly from the oötype, iv) the number of spines per ventrolateral transverse row, and in v) body size and the length/width ratio, vi) the oesophagus and caecal length(s) relative to body total length, vii) the length of the posterior caeca relative to the anterior pair, viii) the testis length/width ratio and its total size relative to that of the body, ix) the postovarian field as a percentage of body length, and x) egg size. In addition, C. beveridgei n. sp. is further differentiated by possessing a female genital pore that opens anterodextral to the male pore while C. bullardi n. sp. differs further in possessing a testis that is almost entirely intercaecal and does not extend anteriorly to the level of the intestinal bifurcation. Employing genetic analysis of ITS2 rDNA sequence data, representing these species and a further 13 recognised and three putative species of Cardicola, we were able to unequivocally confirm these specimens as distinct (9–22% different over 420 nucleotide positions). Distance analysis of ITS2 showed that i) species of Cardicola from the Siganidae formed a monophyletic clade, to the exclusion of other Cardicola species reported from the Scombridae, Sparidae, Lutjanidae and Chaetodontidae, ii) a general phylogenetic isolation exists between the species of Cardicola reported from scombrid fishes, and iii) C. beveridgei n. sp. and Cardicola milleri Nolan & Cribb, 2006 from lutjanids and Cardicola chaetodontis Yamaguti, 1970 from chaetodontids are phylogenetically close, despite the evolutionary remoteness between the host groups and their highly disparate biology. Given the likelihood of many additional species being attributed to Cardicola, we predict that continued molecular analyses will indicate that this genus will prove to incorporate a series of radiations in association with particular fish taxa as well as evidence of host-switching. (Nucleotide sequences reported in this paper are available in the GenBank database under accession no. KF752497).