The phylogenetic analysis of skull characteristics, along with data derived from lung and hemipenial morphology, does not support monophyly of the predominantly terrestrial chamaeleons, Brookesiinae (Brookesia plus Rhampholeon), as sister-taxon of a monophyletic clade of arboreal chamaeleons, the Chamaeleoninae. Instead, the phylogenetic interrelationships of chamaeleonine lizards are (Brookesia (“Rhampholeon” (Bradypodion, Chamaeleo)). The monophyly of the genus Rhampholeon is not demonstrated. The arboreal chamaeleons form a monophyletic group comprising two genera, Bradypodion and Chamaeleo. Bradypodion may be placed as sister-group of the genus Chamaeleo, but its phyletic position and monophyly cannot at present be corroborated.

This study documents that there is a high degree of intraspecific variability in skull characters which may be due to paedomorphic reduction in the skull, especially of small species. Characters affected by a variable degree of ossification include the separation of a prefrontal fontanelle, the contact of the squamosal with the parietal, the size and position of the fenestra vestibuli, the degree of ossification in the basicranial rim of the fenestra, the extent of ossification of the pterygoid wing, and the shape of the skull roof as indicated by the bones forming the dorsal margin of the orbit. The closure of the lateral aperture of the occipital recess might indicate that miniaturization, and concomitant paedomorphosis, may have played a role in the initial phases of chamaeleonine phylogeny.