Aside from their tails, what were the differences between the two groups?
The rhamphorhynchoids had, shorter heads and necks, and all of them had teeth. They ranged in size from small to medium, the largest being the size of sea gulls. The pterodactyloids exhibited several trends in their evolution: loss of teeth, longer heads and necks, development of head crests, longer forearms, and most visibly, increase in size. The largest pterodactyloids were not only far larger than the largest rhamphorhynchoids, they were the largest flying creatures of all time (see below).
