Stegodon remains originating from Late Pleistocene layers of the archaeological cave site Liang Bua on the Indonesian Island of Flores, are described as a new endemic dwarf subspecies: Stegodon florensis insularis subsp. nov. Some fossil Stegodon fragments were found in association with the recently described remains of Homo floresiensis, but many occur in levels with high artefact concentrations. The direct ancestor is the larger-sized S. florensis florensis, known from Early Pleistocene and early Middle Pleistocene sites on Flores. The assemblage from Liang Bua comprises mostly dental and skeletal elements of juvenile individuals. S.f. insularis is characterized by an advanced molar ridge formula and diminutive size: on average the molars are 30 per cent smaller in linear dimensions as compared to the ancestral species. Hominin activities are likely to have played a role in the Stegodon bone accumulation at Liang Bua.