The behaviour of cryptic tropical forest ungulates that are not identifiable from unique coat colour and patterns often impedes detectability and investigations of population density, which underpin conservation plans. The shy and endangered Bornean banteng has a declining trend, but quantifying this requires sufficient detections to estimate robust population parameters, which are currently unavailable. Using intensive camera trapping and individual identification from natural marks by two observers, we estimated the baseline population density of Bornean bantengs in Malua and Tabin forests in Sabah (Malaysian Borneo) using a spatially explicit capture-recapture framework. We also investigated the efficacy of two commonly-used survey methods (camera trapping and signs) that have previously failed to detect the species, by contrasting capture frequencies to estimate the probability of odds of capture. Density estimates and simulated 95% confidence limits were exceptionally low in both forests and with negligible differences arising from small disparities in the interpretation of natural marks. Density in Malua ranged from 0.5 individuals per 100 km2 (0.21–1.48) to 0.56 (0.15–2.09), and in Tabin between 0.61 (0.32–1.16) to 0.95 (0.54–1.66). The capture odds were significantly greater for camera traps (X2 = 20, p < 0.001, and OR = > 4, p < 0.001); sign survey efficacy declined at higher elevations and under dense canopy. Using natural marks for individual identification was resource-demanding, but provided robust population density parameters for an otherwise challenging species to detect. Extremely low-density estimates of Bornean bantengs highlights the urgency for greater control of poaching, which is almost certainly decimating the population. Rapid implementation of actions to mitigate against further losses are essential for halting the declining trend. The estimation of density parameters in other forests in Sabah that contain bantengs would set the context for our density estimates. It would additionally provide a basis for long-term population monitoring, and facilitate investigations into the effectiveness of enforcement strategies.