A population and habitat viability analysis (PHVA) was carried out for the Malagasy giant jumping rat (Hypogeomys antimena), one of the key species of the highly threatened dry deciduous forests on the western coast of Madagascar. The occurrence of H. antimena is now confined to 200 km2 of fragmented but relatively undisturbed forest remnants, divided in northern and southern subpopulations. Since 1985 the habitat has declined by about 52% (1985: 42,000 ha; 2000: 20,000 ha). The annual rate of habitat decline increased from 3.9% between 1985 and 1995 to 4.4% between 1995 and 2000. Within a study area (Kirindy Forest/CFPF) in the southern subpopulation, the Hypogeomys population collapsed during the decade 1990–2000, as well as over its remaining range. An ongoing population decline within the next 100 years is predicted even if further habitat decline can be stopped within the next 5 years and no additional mortality by roaming dogs is considered. Thereby, the outcomes of two different individual-based simulation approaches, one that was explicitly written to reflect Hypogeomys life history and VORTEX, one of the most common software packages used for this purpose, were compared. The results of the Hypogeomys model were more pessimistic, but were within the range of predictions of the VORTEX model which calculated larger standard deviations of the mean values. In both subpopulations, a slight increase in the mortality caused by roaming dogs resulted in a predicted decline to an average population size of maximal 170 individuals within 100 years with a high risk of extinction. However, the simulations indicated that the most important factor is reduction in habitat. If the actual annual rate of habitat lost continues, the extinction of the both subpopulations and therefore the entire species is predicted within 24 years.