There are limited reports of infectious agents affecting Australian cowtail stingrays. In the present study, a new species of ascaridoid nematode belonging to the genus Mawsonascaris is described. The most distinct characteristic features were observed in females (the presence of a polar spine in the eggs and a flap‐like projection in the vulval area). An identification key for Mawsonascaris spp. is provided. Additionally, internal transcribed spacers (ITS) sequences were obtained for the new species. Alignment of the ITS sequence of the specimens in the present study with those deposited in GenBank showed that there exists no other highly similar sequence. Phylogenetic analyses resulted in a distinct grouping of our specimens supporting morphological distinction from previously described Mawsonascaris spp. Histology was used to investigate the pathology caused by the infection. Necrosis, inflammation and fibrosis were evident at the border of the nodules formed by parasite. A large number of parasites were present in muscularis mucosae and submucosa but not in the muscularis of the stomach. The parasites were associated with an increased inflammatory response, which was also found in the muscularis mucosae and submucosa. Similar pathology has been described in elasmobranchs infected by cestodes, although with more severe lesions.