Invasive non-native species are of great concern throughout the world. Potential severity of the impacts of non-native species is assessed for effective conservation managements. However, such risk assessment is often difficult, and underestimating possible harm can cause substantial issues. Here, we document catastrophic decline of a soil ecosystem in the Ogasawara Islands, a UNESCO World Heritage site, due to predation by non-native land nemertine Geonemertes pelaensis of which harm has been previously unnoticed. This nemertine is widely distributed in tropical regions, and no study has shown that it feeds on arthropods. However, we experimentally confirmed that G. pelaensis predates various arthropod groups. Soil fauna of Ogasawara was originally dominated by isopods and amphipods, but our surveys in the southern parts of Hahajima Island showed that these became extremely scarce in the areas invaded by G. pelaensis. Carnivorous arthropods decreased by indirect effects of its predation. Radical decline of soil arthropods since the 1980s on Chichijima Island was also caused by G. pelaensis and was first recorded in 1981. Thus, the soil ecosystem was already seriously damaged in Ogasawara by the nemertine. The present findings raise an issue and limitation in recognizing threats of non-native species.