Eleven named species are within the genus Pegivirus.

[2] Isolates belonging to the species Pegivirus C are monophyletic and show < 50% nucleotide (55% amino acid) sequence divergence between aligned sequences from the polyprotein from each other.

However, all differ by >50% nucleotide (>55% amino acid) divergence from other members of this genus.

This sequence differs by >50% nucleotide (>55% amino acid) divergence from all proposed members of the primate-derived Pegivirus C species that originate from primate host species (humans, chimpanzees, and several New World monkey species).

[citation needed] The use of deep sequencing technologies has identified additional viruses that differ from Pegivirus B species by >50% nucleotide (>55% amino acid) and Pegivirus C in rodents, horses, and in different bat species, and Old World monkeys and the number of Pegivirus species has been expanded to eleven.