1. Assemblage similarity decays with geographic distance—a pattern known as the distance-decay relationship. While this pattern has been investigated for a wide range of organisms, ecosystems, and geographical gradients, whether these changes vary more cryptically across different forest strata (from ground to canopy) remains elusive. 2. Here, we investigated the influence of ground vs arboreal assemblages to the general distance-decay relationship observed in forests. We seek to explain differences in distance-decay relationships between strata in the context of the vertical stratification of assemblage composition, richness, and abundance. 3. We surveyed for a climate sensitive model organism, amphibians, across vertical rainforest strata in Madagascar. For each tree, we defined assemblages of ground-dwelling, understory, or canopy species. We calculated horizontal distance-decay in similarity across all trees, and across assemblages of species found in different forest strata (ground, understory, and canopy). 4. We demonstrate that within stratum comparisons exhibit a classic distance-decay relationship for canopy and understory communities but no distance-decay relationships for ground communities. We suggest that differences in horizontal turnover between strata may be due to local scale habitat and resource heterogeneity in the canopy, or the influence of arboreal traits on species dispersal and distribution. 5. Synthesis: Biodiversity patterns in horizontal space were not consistent across vertical space, suggesting that canopy fauna may not play by the same set of ‘rules’ as their conspecifics living below them on the ground. Our study provides compelling evidence that the above-ground amphibian assemblage of tropical rainforests is the primary driver of the classical distance-decay relationship.