ABSTRACT. Habitat loss and fragmentation are considered to be the most important factors responsible for population decreases in small mammal populations. Particularly important is also the effect of insularity that can act syn-ergistically with the previous factors. Population Viability Analysis (PVA) combines the spatial component of the problem with the species population structure offering an integrated platform for testing and assessing the effects of critical parameters upon the population viability. Various management options can also be quantified and tested. In the case of Sciurus anomalous, a vulnerable squirrel species endemic in Lesvos, a series of threats and management problems were identified and assessed. A stochastic simulation model was developed and parameterized with field data for the species using the program Ramas/GIS. The results suggested that special attention has to be paid to the planning of road system networks and to stopping illegal hunting, especially when extinction risks for vulnerable populations are higher with the above threats.