Knowledge of the biogeography of marine taxa has lagged significantly behind terrestrial ecosystems. A hotspot of marine biodiversity associated with coral reefs is known in the Coral Triangle of the Indo-West Pacific, but until now there was little data with which to evaluate broad patterns of species richness in the coastal fauna of ecosystems other than coral reefs. This data is critically needed for fauna with low functional redundancy like that of mangroves, that are vulnerable to habitat loss and rising sea levels. Here we show that the diversity of mangrove fauna is characterized by two distinct hotspots in the Indo-West Pacific, associated with two habitat types: fringe mangroves in the Coral Triangle, and riverine mangroves in the Strait of Malacca, between the west coast of Peninsular Malaysia and Sumatra. This finding, based on a family of slugs of which the systematics has been completely revised, illustrates an unexpected biogeographic pattern that emerged only after this taxon was studied intensively. Most organisms that live in the mangrove forests of Southeast Asia remain poorly known both taxonomically and ecologically, and the hotspot of diversity of onchidiid slugs in the riverine mangroves of the Strait of Malacca indicates that further biodiversity studies are needed to support effective conservation of mangrove biodiversity.