Cylicospirura is a genus of spirocercid nematodes infecting felids around the globe. Eleven species have been characterised, with C. felineus and C. subaequalis being reported in jaguarundis, Herpailurus yagouaroundi, from Brazil. Herein, we described spirocercid reddish worms collected from three jaguarundis from Costa Rica by using hierarchical clustering and dendrogram plots of morphological characters reported from our specimens and compared to other Cylicospirura spp., histopathological observations of associated lesions, and phylogenetic analyses of both mitochondrial and ribosomal loci. Nematodes were found within stomach nodules located in the submucosa causing a pyogranulomatous, multifocal, nodular, and sclerosing gastritis. In addition, the collected worms differed from their congeners by having a longer body and smaller muscular and glandular oesophagus, subsequently showing lower total oesophagus to body length percentage and ratio of glandular to muscular oesophagus. Cytochrome oxidase subunit 1 and internal transcribed spacer 1 analyses revealed that worms were 8.33 to 8.66% different from C. felineus, C. subaequalis, or C. petrowi and 15.2 to 15.4% different from C. petrowi, respectively. Moreover, sequences derived from collected worms clustered separately from other Cylicospirura spp. available in GenBank® in the phylogenetic trees. By using an integrative taxonomy approach, the nematodes collected from stomach nodules of jaguarundis were described as a new taxon, for which the name Cylicospirura wishkai sp. nov. is proposed.