Adansonia rubrostipa (MALVACEAE family) is a threatened endemic baobab tree species of western Madagascar that is classified as a species of least concern (LC) on the IUCN Red List. Due to increased agricultural activity, its habitat is being modified and degraded. To assess the impact of habitat fragmentation on the generative growth of Adansonia rubrostipa, this initial study was undertaken. The production of fruits and seeds was compared during the fruiting period at four sites: 2 sites in undisturbed habitat (the Andranomena Special Reserve and Ampataka Forest) and 2 sites in disturbed habitat (Andranomena and Mangily villages) by using Generalized Linear Model (GLM). Our results showed that fruit and seed production differed significantly between the two types of habitats. Fruit production was significantly higher among individuals in the disturbed habitat than individuals in the undisturbed habitat (GLM: Wald Χ2 = 31.475, df = 1, p < 0.001), while seed production per fruit was markedly higher among individuals in the undisturbed habitat than individuals in the disturbed habitat although not statistically significant. It seems that A. rubrostipa trees outside forest counterbalance the lower seed number per fruit by higher fruit production. However, this counterbalance mechanism may be not enough considering further forest habitat degradation. Therefore, it should be emphasized that forest fragmentation affects the generative reproduction of Adansonia rubrostipa. We recommend to develop conservation measures based on the theory of sustainable development in agricultural landscapes to maintain the baobab populations in good conditions in the future.