Abstract. Countries in south-eastern Europe are cooperating to conserve a sub-endemic lynx species, Lynx lynx martinoi. Yet, the planning of species conservation should go hand-in-hand with the planning and management of (new) protected areas. Lynx lynx martinoi has a small, fragmented distribution with a small total population size and an endangered population. This study combines species distribution modelling with spatial prioritisation techniques to identify conservation areas for Lynx lynx martinoi. The aim was to determine locations of high probability of occurrence for the lynx, to potentially increase current protected areas by 20 % in Albania, the former Yugoslav Republic of Macedonia, Montenegro, and Kosovo. The species distribution modelling used generalised linear models with lynx occurrence and pseudo-absence data. Two models were developed and fitted using the lynx data: one based on natural factors, and the second based on factors associated with human disturbance. The Zonation conservation planning software was then used to undertake spatial prioritisations of the landscape using the first model composed of natural factors as a biological feature, and (inverted) a second model composed of anthropological factors such as a cost layer. The first model included environmental factors as elevation, terrain ruggedness index, woodland and shrub land, and food factor as chamois prey (occurrences) and had a prediction accuracy of 82 %. Second model included anthropological factors as agricultural land and had a prediction accuracy of 65 %. Prioritised areas for extending protected areas for lynx conservation were found primarily in the Albania–Macedonia–Kosovo and Montenegro–Albania–Kosovo cross-border areas. We show how natural and human factors can be incorporated into spatially prioritising conservation areas on a landscape level. Our results show the importance of expanding the existing protected areas in cross-border areas of core lynx habitat. The priority of these cross-border areas highlight the importance international cooperation can play in designing and implementing a coherent and long-term conservation plan including a species conservation plan to securing the future of the lynx.