Mitochondrial genomes (mtDNA) of animals are circular molecules of relatively small size, compactly organized, and generally encoding genes for 2 rRNAs, 22 tRNAs, and 13 proteins that are required for mitochondrial function. Methods of mtDNA isolation take advantage of its physical localization apart from the nuclear genome (centrifugation at low speed efficiently separates mitochondria from nuclei) and of its structure (alkaline lysis differentially precipitates linear nuclear DNA, but not circular mtDNA). Furthermore, the recent development of robust long-PCR techniques has boosted high-throughput determination of complete sequences of animal mtDNAs. The exponentially growing number of complete animal mitochondrial genomes deposited in GenBank allows a phylogenomic approach to disentangle phylogenetic relationships among main animal phyla, and provides extensive new data to gain insights on the molecular mechanisms underlying genome evolution.