They're the only animals that still exhibit a true diapsid skull morphology. Ancestral tetrapods were divided roughly into ones with two holes behind the eye orbit and one hole behind the orbit. read more
And, as Lorri pointed out, they have a third eye one the top of their head. It's not really functional anymore, but it's the thought that counts. There's more non-skeletal features as well. They're definitely not lizards; they definitely are weird. read more
The main reason why tuatara are not classified as lizards are: * Tuatara have a membranous third eyelid, which is not present in lizards. * Lizards have external ears, but tuatara lack ears, and have no ear drum, ear holes or middle ear cavity. read more
The tuatara is considered the most unspecialised living amniote; the brain and mode of locomotion resemble those of amphibians and the heart is more primitive than that of any other reptile. The lungs have a single chamber and lack bronchi. read more