Context The Sunda clouded leopard is vulnerable to forest loss and fragmentation. Conservation of this species requires spatially explicit evaluations of the effects of landscape patterns on genetic diversity, population size and landscape connectivity. Objectives We sought to develop predictions of Sunda clouded leopard population density, genetic diversity and population connectivity across the state of Sabah, Malaysian Borneo. We also wished to quantify the differences in connectivity metrics from an empirically optimized model of landscape resistance with one based on expert opinion. Methods We investigated connectivity metrics for Sunda clouded leopards across Sabah, based on an empirically optimised, movement based model, and an expert-opinion derived model. We used simulation modelling to predict and compare the patterns and causes of differences in the local neighbourhood population density, distribution, and genetic diversity across the two different resistance maps, at two dispersal distances. Results The empirical model produced higher estimates of population size, population density, genetic diversity and overall connectivity than the expert-opinion model. The overall pattern of predicted connectivity was similar between models. Both models identified a large patch of core habitat with high predicted connectivity in Sabah’s central forest region, and agreed on the location and extent of the main isolated habitat fragments. Conclusions We identified clear relationships between landscape composition and configuration and predicted distribution, density, genetic diversity and connectivity of Sunda clouded leopard populations. Core areas are comprised of large and unfragmented forest blocks, and areas of reduced forest cover comprise barriers among patches of predicted remaining habitat.