A total of 1981 bp of the mitochondrial 16S rRNA, 12S rRNA and cytochrome b genes were analyzed in five boine and one pythonine snake species to determine phylogenetic relationships between Malagasy and Neotropical taxa included in the genus Boa. The obtained cladograms significantly grouped Boa constrictor with the Neotropical genera Eunectes and Epicrates, whereas the Malagasy species were the sister group of the clade of the three Neotropical taxa. Based on these results, Sanzinia and Acrantophis should be considered as valid generic names for the Malagasy boas. Their origin may be a result of a Cenozoic dispersal from Africa or Asia.