Asian rainforests suffer from massive deforestation but remain less studied pantropically. Although Sri Lanka is a severely threatened biodiversity hot spot with high endemicity and unique conservation challenges, few have investigated how fauna respond to environmental perturbations caused by human modification of habitats. We investigated differences in the diversity and community composition of amphibians and butterflies in primary and selectively logged forests (SLF), home gardens and plantations in the Sinharaja lowland tropical forest and surrounding areas. A Bayesian multi-model inference approach was then used to identify environmental variables that explained differences in richness and abundance patterns among sites. Amphibian species richness (SPR) was highest in a forest habitat, and community composition differed between forest and disturbed habitats. In contrast, butterfly SPR increased with increasing disturbance. Butterfly diversity patterns were best explained by climatic variables, while structural habitat parameters were the best predictors of amphibian patterns. Based on research findings, the protection of primary forest habitats is essential for amphibian conservation. Regenerating SLF can be of high conservation value especially if substantial pristine habitat remains conserved in the landscape. Anthropogenic habitats at the periphery of forests require realistic management recommendations to support the species inhabiting, visiting or migrating through them. Different environmental predictors for butterflies and amphibians underscore the importance of including multiple indicator taxa in surveys that are intended to inform habitat management.