Most studies that examine the influence of climatic change on flora and fauna have focused on northern latitudes; however, there is increasing recognition that tropical regions are also being affected. Despite this, regions such as Madagascar, which are rich in endemic biodiversity but may have low adaptive capacity to climatic change, are poorly represented in studies examining the effects of climate variability on biota. We investigated how El Niño Southern Oscillations (ENSO) influence precipitation patterns in the rainforest region of southeastern Madagascar (1962–2006) and then constructed models to assess the potential contribution of climatic variables on the reproductive parameters of the Milne Edward's sifaka, a threatened lemur species (Propithecus edwardsi), over a 20-year period. The Southern Oscillation Index of sea surface temperature (SST) anomalies in the tropical Pacific was associated with precipitation patterns including wetter wet seasons during warmer phases and drier dry seasons following cooler phases. The best-supported models of lemur fecundity (female offspring per female that survive to 1 year of age per year) included cyclone presence during gestation and ENSO phase before conception and during the first 6 months of life. Models also suggested that heavy rains during gestation may limit birth rates and that prolonged drought during female lactation may limit first year offspring survival; although these variables were given little importance for predicting overall fecundity relative to ENSO phases and cyclone presence. Our results linking lemur reproduction with climatic variability suggest that climatic changes may be an additional threat to Madagascar's unique and already endangered flora and fauna. The association between precipitation in southeastern Madagascar and SST anomalies in the tropical Pacific suggests that dynamics of wildlife populations even in tropical areas such as Madagascar can be affected by global climate cycles making them potentially vulnerable to global climate change.