Roundworms (Ascaridida: Nematoda), one of the most common soil-transmitted helminths (STHs), can cause ascariasis in various hosts worldwide, ranging from wild to domestic animals and humans. Despite the veterinary and health importance of the Ascaridida species, little or no attention has been paid to roundworms infecting wild animals including non-human primates due to the current taxon sampling and survey bias in this order. Importantly, there has been considerable controversy over the years as to whether Ascaris species infecting non-human primates are the same as or distinct from Ascaris lumbricoides infecting humans. Herein, we first characterized the complete mitochondrial genomes of two representative Ascaris isolates derived from two non-human primates, namely, chimpanzees (Pan troglodytes) and gibbons (Hylobates hoolock), in a zoological garden of southwest China and compared them with those of A. lumbricoides and the congeneric Ascaris suum as well as other related species in the same order, and then used comparative mitogenomics, genome-wide nucleotide sequence identity analysis, and phylogeny to determine whether the parasites from chimpanzees and gibbons represent a single species and share genetic similarity with A. lumbricoides. Taken together, our results yielded strong statistical support for the hypothesis that the chimpanzee- and gibbon-derived Ascaris represent a single species that is genetically similar to A. lumbricoides, consistent with the results of previous morphological and molecular studies. Our finding should enhance public alertness to roundworms originating from chimpanzees and gibbons and the mtDNA data presented here also serves to enrich the resource of markers that can be used in molecular diagnostic, systematic, population genetic, and evolutionary biological studies of parasitic nematodes from either wild or domestic hosts.