ADAMTS, constituting a recently discovered family of secreted zinc-dependent metalloproteases, have been shown to have critical physiological roles through identification of a number of natural animal and human gene mutations. The identification of six ADAMTS genes in the basal chordate Ciona intestinalis provides new insight into how, when and in what order the vertebrate orthologues have evolved. The phylogenetic assignments, based on sequences conserved across all genes, are supported by conserved domain structures within defined sub-families. The phylogeny and the frequent localisation of ADAMTS genes in paralogous regions of the genome are consistent with the vertebrate lineages having arisen by large scale or genome duplication. The high level of conservation in the protease active site of vertebrate orthologues within some sub-families suggests subfunctionalisation, whereas the greater divergence in others would favour the evolution of novel substrate specificities and these observations are borne-out where substrate-specificity is known. The expansion and sub-specialization of the ADAMTS family is a component of the increased complexity of extracellular matrix that is associated with the evolution of vertebrates.