Anisakid nematodes have been identified in a wide variety of fish and marine mammal species. In Brazil, Anisakis physeteris, A. insignis, A. typica, A. nascetti, and those of the A. simplex complex have been reported infecting fishes and cetaceans. In this study, specimens collected from a dwarf sperm whale Kogia sima (Owen, 1866) stranded on the northeastern coast of Brazil were identified through morphological and genetic analyses as A. paggiae. Anisakids were examined through differential interference contrast light and scanning electron microscopy (SEM). Morphological and morphometric analysis revealed that these specimens belonged to Anisakis sp. clade II and more specifically to A. paggiae, exhibiting a violin-shaped ventriculus and 3 denticulate caudal plates, which are taxonomic characters considered unique to this species. Genetic analysis based on the mtDNA cox2 gene confirmed our identification of A. paggiae. Phylogenetic trees using both maximum likelihood and neighbor-joining methods revealed a strongly supported monophyletic clade (bootstrap support = 100%) with all available A. paggiae sequences. Integrative taxonomic analysis allowed the identification of A. paggiae for the first time in Brazilian waters, providing new data about their geographical distribution. Moreover, here we present the first SEM images of this species.