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The nematode family Spirocercidae Chitwood and Wehr, 1932, comprises three subfamilies, Spirocercinae Chitwood and Wehr, 1932; Ascaropsinae Alicata and McIntosh, 1933; and Mastophorinae Quentin, 1970, which occur worldwide. Spirocercids infect canids and can cause severe illness. The crab-eating fox, Cerdocyon thous (Linnaeus, 1766), is a canid that inhabits most of South America, including Brazil and is a host for several parasitic worms, in particular, nematodes. However, few reports or genetic data are available on the spirocercids found in this host. In the present study, we describe a new species of Spirobakerus Chabaud and Bain 1981, from the intestine of two crab-eating foxes from two different biomes in Brazil. Spirobakerus sagittalis sp. nov. presents a) unequal spicules, with a long, thin left spicule with a lanceolated shape at the tip; b) a pair of sessile papillae and a median unpaired papillae located anteriorly of the cloaca, and c) a tuft without spines at the tip of the tail in females. The molecular phylogenetic analysis indicated that S. sagittalis sp. nov. is basal to the other species of the subfamily Ascaropsinae, which was not recovered as monophyletic. Our phylogenies also indicated that Spirocercidae is paraphyletic, given that Mastophorinae did not group with Ascaropsinae and Spirocercinae. We provide the first molecular data on the genus Spirobakerus and expand the molecular database of the spirocercids. However, further studies, including the sequences of other spirocercid taxa, are still needed to infer the relationships within this family more accurately.