Ecological communities and biodiversity are shaped by both abiotic and biotic factors. This is well illustrated by extreme environments and invasive species. With global change, hydrogen sulphide is an increasing threat for many multicellular organisms. As the formation, size, and abundance of hydrogen sulphide-rich marine environments increase, many species are challenged with the inhibiting effect of sulphide on the aerobic energy production via cytochrome c oxidase, ultimately causing the death of the organism. Interestingly, many protist, yeast, plant, and also animal species possess a sulphide-resistant alternative oxidase (AOX). In this study, we investigated whether AOX is functionally involved in sulphide stress response of the highly invasive marine tunicate, Ciona intestinalis. At the LC50, the sulphide effect on developmental success of AOX knock-down Ciona embryos was three times stronger than on control groups. Further, AOX mRNA levels were higher under sulphide than control conditions - and this effect increased with embryonic development. Together, we found that AOX is indeed functionally involved in the sulphide tolerance of Ciona embryos, hence, very likely contributing to its invasive potential; and that AOX tends to underlie transcriptional control. We suggest that AOX-possessing species play an important role in shaping marine ecological communities, and this importance may increase under ongoing global change.