Sponges (Porifera) are the most primitive multicellular animals that are highly diverse and complex associated with other organisms, microbes especially. Recently, sponges have received a lot of attention as they are a rich source of nature products with antiviral, antitumor, and antimicrobial activities. Sponges play such important roles in so many marine habitats but little is known about their diversity, biology and ecology as compared with most other animal groups. Moreover, due to limited information provided based on morphology, other method of classification is need. Mitochondrial DNA sequence may fulfill such purpose. The complete nucleotide sequence (19444 bp) of the mt genome of the Cinachyrella australiensis (Demospongiae: Spirophorida) was determined. The genome contains the two rRNA, 24 tRNA and 14 protein-coding genes. We found that poriferan mtDNAs resemble those of other animals in their compact organization, and a well-conserved animal-like gene order. However, this molecule has several unique features: the ATP 9 gene is the first found to be present in the mt genome of multicellular animals, the cytochrome c oxidase subunit I (COI) gene include a group I intron, and encode bacteria-like tRNA. The results represent that the evolution of metazoan mtDNA has been a multistep process to the reduction of tRNA and the introduction of multiple changes of the translation code.