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This species is the sister species of Apis koschevnikovi, and both are in the same subgenus as the Western (European) honey bee, Apis mellifera.
In the modern clade Anurognathidae, Anurognathus is the sister taxon of the clade Asiaticognathidae, which contains the species Batrachognathus, Dendrorhynchoides and Jeholopterus.
Evidence was published in a 2013 molecular study which showed that it was the sister taxon to the Australian Magpie (C. tibicen).
Phylogenetic analysis of the mitochondrial 16S ribosomal RNA gene and a range of other anomuran crustaceans, using Bayesian inference, places this species from the East Scotia Ridge as a sister taxon to Kiwa hirsuta, with a sequence divergence from this species of 6.45%, which is consistent for within-genus divergence in squat lobsters.
Nuclear DNA sequence analysis has indicated that it is a sister taxon to Rhagomys.
When herpetologist G. K. Noble examined Allophryne, he suggested it was closely related to glassfrogs, a hypothesis later confirmed by recent phylogenetic studies, which have found Allophryne is the sister taxon of the glassfrog clade Centroleninae.