Complete or nearly complete nucleotide sequences of mitochondrial genomes (mtDNAs) were determined from eight species which, together with previous mtDNA data for two other taxa, cover most subfamilies of Iguanidae sensu lato. These iguanid mtDNAs were found to be rather conservative with respect to gene arrangements and molecular evolutionary rates, which contrasts with mtDNAs of Acrodonta (Agamidae and Chamaeleonidae) in which several gene rearrangements and highly accelerated molecular evolutionary rates have been known. Phylogenetic analyses consistently suggested the earliest shoot-off of a Malagasy subfamily Oplurinae and an affinity of Polychrotinae and Tropidurinae sensu stricto. However, even with the ample molecular characters derived from complete mtDNA sequences, phylogenetic relationships between iguanid subfamilies were poorly resolved in general, presumably due to the rapid ancient cladogenesis. Divergence time estimation without assuming the molecular clock suggested the Late Triassic/Early Jurassic divergence of Iguanidae from acrodonts and the Middle/Late Jurassic divergence of Oplurinae from the other iguanids. Together with geological and paleontological evidence, these results led us to propose Gondwanan vicariance for the origin of Malagasy oplurines without invoking a land bridge connection between South America/Antarctica and drifting Madagascar/India.