The spectacular diversity of sub-Saharan Africa's large mammals was hit by constant social strife and civil war over three decades (1970s-1990s) leading to localized extinctions and drastic reductions in population sizes for many species. These localized extinctions and reduction in population sizes undermine the ability of species to evolve and adapt to changing environments as a result of genetic erosion. The genetic consequences of the widespread reduction of population sizes as a result of social strife in sub-Saharan Africa are not well documented. Here we review past molecular genetic data that are relevant to understanding of the genetic effects of war and social strife on Africa's wildlife. Uganda was probably one of the worst affected countries. Before 1972, Uganda had large herds and a variety of mammals. However, following the breakdown of law and order, some large mammals were exterminated while other populations were decimated. Recent results of genetic surveys in five large mammals in Uganda (the common warthog, savanna elephant, savanna buffalo, common hippopotamus and Uganda kob) suggest a substantial erosion of genetic diversity in the elephants and warthogs of Queen Elizabeth National Park. Although the rest of the studied mammals show no direct loss of genetic diversity, strong genetic differentiation was observed among most populations separated by even short geographical distances, indicating an increase in the 'between' component of genetic diversity that could have been accelerated by genetic erosion due to decrease in population sizes.