Alternative oxidase (AOX), a ubiquinol oxidase, introduces a branch pathway to the respiratory electron transport chain (ETC), bypassing complexes III and IV and catalysing the cyanide-resistant reduction of oxygen to water without translocation of protons across the inner mitochondrial membrane. Thus, it functions as a non-energy-conserving member of respiratory ETC. Previous studies of AOX focused on plants and some fungi, whereas data on animals are limited. In this study, full-length AOX cDNA was cloned from the Echiuran worm, Urechis unicinctus, a marine benthic invertebrate. In addition, mRNA expression pattern of combined activity of cytochrome c oxidase (CCO) in the body wall and hindgut of the worm exposed in sulphide (50 µM and 150 µM) was measured. The results revealed that AOX mRNA expression increased in a time- and concentration-dependent manner in both tissues, was significantly increased at 48 h, and continuously increased with time. In contrast, the activity of CCO decreased significantly at 24 h and was inhibited at 48 h during exposure to 150 µM sulphide. The present data indicate the expression of AOX mRNA depended on the sulphide concentration present as well as being influenced by the physical condition of the worm, especially the CCO activity.