Coevolution played a central role in shaping biodiversity. However, coevolutionary events driving reciprocal diversification between interacting partners lack empirical evidences. Examples of diversification arising from mutualisms and antagonisms at different trophic levels are scarce, which limits our understanding on how complex relationships between species arise within communities. By adopting a cophylogenetic framework, we investigated whether congruence in plant-lemur phylogenies are driven by mutualisms and antagonisms in Madagascar, where endemic species have evolved within a unique isolated biogeographical context. Although we found weak support for coevolution, this is not to say that interactions between lemurs and plants did not promote a shared evolutionary history. Weak cophylogenetic signals do not necessarily imply lack of co-diversification. Rather, our results suggest that vertebrates and plants influenced each other evolution through ecological interactions, but in a multi-specific and generalist context where the cophylogenetic process leaded to spatio-temporal asymmetries and shifts between periods of coevolution and independent evolution, ultimately resulting in a weak, continuous and diffuse process.