The neurocranial osteology of the giant monitor lizard Varanus (Megalania) prisca Owen, 1859 is described in detail for the first time. Optimization of neurocranial characters onto phylogenetic topologies for varanoids, including Lanthanotus, Heloderma, and Varanus species nests V. prisca within an Indo-Australian clade of Varanus on the basis of characters of the otic capsule. A sister-taxon relationship between V. prisca and Varanus komodoensis Ouwens, 1912 is proposed based on apomorphies of the crista prootica, fenestra vestibuli, occipital recess, and supraoccipital. These results support a monophyletic clade of giant monitors among Indo-Australian species, and unambiguously synonymize Megalania with Varanus at both generic and subgeneric levels. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155, 445–457.