Loch Creran on the west coast of Scotland supports the most expansive reefs of the serpulid Serpula vermicularis in the world. It also supports flame shell Limaria hians and horse mussel Modiolus modiolus reefs, thereby ensuring this loch received designation as a European Special Area of Conservation in 2005. In 2015, environmental DNA of the invasive, non-native colonial tunicate Didemnum vexillum, which has a worldwide distribution, was detected in Loch Creran. Didemnum vexillum was confirmed as being present at an oyster farm in the sea loch, using the cytochrome oxidase I gene (COI), following rapid intertidal and dive surveys in early September 2016. The abundance and distribution range assessment carried out at the farm indicated an early-stage D. vexillum invasion. The follow up dive surveys and wider loch intertidal surveys carried out in 2017 and 2018 confirmed that the D. vexillum presence continues to be associated exclusively with the oyster farm. This is the first time that such a highly invasive species has been found within a protected area of global significance and it has significant biosecurity and policy implications regarding how to manage such invasive species.