Stonustoxin (SNTX) is a multifunctional lethal protein isolated from venom elaborated by the stonefish, Synanceja horrida. It comprises two subunits, termed alpha and beta, which have respective molecular masses of 71 and 79 kDa. SNTX elicits an array of biological responses both in vitro and in vivo, particularly a potent hypotension that appears to be mediated by the nitric oxide pathway. As a prelude to structure-function studies, we have isolated and sequenced cDNA clones encoding the alpha- and beta-subunits of SNTX from a venom gland cDNA library. The deduced amino acid sequence of neither subunit shows significant homology with any known protein. Protein sequence alignment does, however, show the subunits to be 50% homologous to each other and implies that they may have arisen from a common ancestor. The subunits of this novel toxin lack typical N-terminal signal sequences commonly found in proteins that are secreted via the endoplasmic reticulum-Golgi apparatus pathway, indicating the possibility of its being secreted by a non-classical pathway, which is not clearly understood. The SNTX subunits have been expressed in Escherichia coli as cleavable fusion proteins that cross-react with antibodies raised against the native toxin. To the best of our knowledge, this is the first complete sequence of a fish-derived protein toxin to be reported.