Flying squirrels are monophyletic.

Seven genera of flying squirrels share five characters of wrist anatomy, which form a functional complex associated with the support of the patagium. In these characters, they differ from all genera of tree and ground squirrels examined. Among mammals, gliding membranes have evolved independently in several other groups. The manner of attachment of the patagium to the forelimb is different in each and demonstrates five morphologies differing from that of flying squirrels. This complex wrist anatomy of flying squirrels provides evidence that gliding evolved only once among squirrels and that the flying squirrels are a monophyletic group.