The island of Bawean, Indonesia, is home to the endemic Bawean warty pig Sus verrucosus blouchi and Bawean deer Axis kuhlii. Despite their threatened status, no long-term monitoring programme is in place for either species. Using random encounter and occupancy modelling based on 4,516 camera-trap days in 2014 and 2015 we aimed to provide population estimates and ecological data, including habitat preferences, for these species. For the Bawean warty pig we estimate an overall population size of 234–467 mature individuals and demonstrate a negative correlation between probability of occupancy and distance from villages. This preference for human-modified habitat has implications for human–wildlife conflict and hunting pressure for this species. The population of the Bawean deer could not be estimated because of the low number of encounters, but we suggest that this indicates the population is considerably smaller than previously reported. As island endemics, the Bawean warty pig and Bawean deer are particularly vulnerable to threats, and appropriate measures for safeguarding the species need to be taken.