The genusSpirocercaincludes nematodes that parasitize the stomach and the oesophagus of carnivores, chiefly canids. Herein, we provide new data about the morphological, histopathological, and molecular characterization ofSpirocercasp. in Andean foxes (Lycalopex culpaeus) in Chile. Intact immature worms, identified asSpirocercasp., were recovered in the lumen of the stomach from two foxes. Histologically, worms morphologically consistent with spirurid nematodes were present within the wall of the stomach and surrounded by nodular areas of inflammation with central necrotic debris. Molecular analysis of thecox1 gene yielded 19 sequences and 5 nucleotide sequence types with 99.95 to 99.98% similarity, being shared between both foxes. Nucleotide similarity ranged from 93.1 (with genotype 2 ofS. lupiandS. vulpis) to 95.8% (with genotype 1 ofS. lupi), a higher similarity than noted from sequences ofS. lupifrom an Andean fox from Peru (91.0 to 93.3%). However, the Poisson Tree Processes for species delineation did not support the existence of a new speciesSpirocerca. Phylogenetic and nucleotide analyses suggest that these specimens belong to a new variant or genotype ofS. lupior to a cryptic species. Whether the presence of the worms in the stomach has to do with genotypic differences in parasites or host or some combination is uncertain.Spirocerca lupihas never been found in Chilean dogs and must be investigated.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00436-023-07825-3.