The black and white ruffed lemur, Varecia variegata, which is endemic to Madagascar, is under the threat of extinction due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Behavioural researchers studying a population of V. variegata inhabiting the Manombo Special Reserve, noted that over a 4-year period, none of the family groups within the reserve produced offspring while those in neighbouring populations had been reproductively successful. Inbreeding depression was postulated as the trigger for this occurrence. However, another explanation exists. A cyclone, striking the region in 1997, destroyed a large percentage of the mature fruit-producing trees that V. variegata relied upon as a food source, which is likely to have produced a nutritional deficit. A panel of 25 simple sequence repeat (SSR) markers was utilised to assess the genetic diversity within four V. variegata populations, including individuals from Manombo and three other populations in southeastern Madagascar. The data revealed that the level of genetic diversity apparent within the Manombo population is comparable to the other groups studied. Therefore, it seems probable that genetic factors are not responsible for the recent lack of reproductive success on the part of the V. variegata at Manombo Special Reserve.