Closely related species tend to be more similar than randomly selected species from the same phylogenetic tree. This pattern, known as a phylogenetic signal, has been extensively studied for intrinsic (e.g. morphology), as well as extrinsic (e.g. climatic preferences), properties but less so for ecological interactions. Phylogenetic signals of species interactions (i.e. resource use) can vary across time and space, but the causes behind such variations across broader spatial extents remain elusive. Here, we evaluated how current and historical climates influence phylogenetic signals of bat-fruit interaction networks across the Neotropics. We performed a model selection relating the phylogenetic signals of each trophic level (bats and plants) with a set of current and historical climatic factors deemed ecologically important in shaping biotic interactions. Bat and plant phylogenetic signals in bat-fruit interaction networks varied little with climatic factors, although bat phylogenetic signals positively covaried with annual precipitation. These findings indicated that water availability could increase resource availability, favouring higher niche partitioning of trophic resources among bat species and hence bat phylogenetic signals across bat-fruit interaction networks. Overall, our study advances our understanding of the spatial dynamics of bat-fruit interactions by highlighting the association of current climatic factors with phylogenetic patterns of biotic interactions.