This study provides a Borneo-wide, quantitative assessment of botanical richness and endemicity at a high spatial resolution, and based on actual collection data. To overcome the bias in collection effort, and to be able to predict the presence and absence of species, even for areas where no collections have been made, we constructed species distribution models (SDMs) for all species taxonomically revised in Flora Malesiana. Species richness and endemicity maps were based on 1439 significant SDMs. Mapping of the residuals of the richness-endemicity relationship identified areas with higher levels of endemicity than can be expected on the basis of species richness, the endemicity hotspots. We were able to identify one previously unknown region of high diversity, the high mountain peaks of East Kalimantan; and two additional endemicity hotspots, the Müller Mountains and the Sangkulirang peninsula. The areas of high diversity and endemicity were characterized by a relatively small range in annual temperature, but with seasonality in temperatures within that range. Furthermore, these areas were least affected by El Niño Southern Oscillation drought events. The endemicity hotspots were found in areas, which were ecologically distinct in altitude, edaphic conditions, annual precipitation, or a combination of these factors. These results can be used to guide conservation efforts of the highly threatened forests of Borneo.