Aptorchis megacetabulus n. sp. is described from the intestine of the northern long-necked turtle, Chelodina rugosa (Pleurodira: Chelidae), in Northern Territory, Australia. This is the first helminth species reported from C. rugosa. This plagiorchioidean digenean differs from the 3 previously known species of Aptorchis in the relative size of the ventral sucker, overall body proportions, nature of the cirrus sac, and egg size. Comparison of approximately 2,700 bases of ribosomal DNA obtained from all known Aptorchis species strongly supports the status of Aptorchis megacetabulus n. sp. as a new species.