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Abstract Climate change is one of the major drivers of biodiversity loss. Among vertebrates, amphibians are one of the more sensitive groups to climate change due to their unique ecology, habitat requirements, narrow thermal tolerance and relatively limited dispersal abilities. We projected the influence of climate change on an endemic toad, Malabar Tree Toad (Pedostibes tuberculosus; hereafter MTT) from the Western Ghats biodiversity hotspot, India, for two different shared socio-economic pathways (SSP) using multiple modeling approaches for current and future (2061–2080) scenarios. The data used predominantly comes from a citizen science program, ‘Mapping Malabar Tree Toad’ which is a part of the Frog Watch citizen science program, India Biodiversity Portal. We also evaluated the availability of suitable habitats for the MTT in Protected Areas (PAs) under the current and future scenarios. Our results show that annual precipitation was the most important bioclimatic variable influencing the distribution of MTT. We used MaxEnt (MEM) and Ensemble (ESM) modeling algorithms. The predicted distribution of MTT with selected environmental layers using MEM was 4556.95 km2 while using ESM was 18,563.76 km2. Overlaying PA boundaries on predicted distribution showed 37 PAs with 32.7% (1491.37 km2) and 44 PAs with 21.9% (4066.25 km2) coverage for MEM and ESM respectively. Among eight future climate scenarios, scenarios with high emissions showed a decreased distribution range from 33.5 to 68.7% of predicted distribution in PAs, while scenarios with low emissions showed an increased distribution range from 1.9 to 111.3% in PAs. PAs from the Central Western Ghats lose most suitable areas with a shift of suitable habitats towards the Southern Western Ghats. This suggests that MTT distribution may be restricted in the future and existing PAs may not be sufficient to conserve their habitats. Restricted and discontinuous distribution along with climate change can limit the dispersal and persistence of MTT populations, thus enhanced surveys of MTT habitats within and outside the PAs of the Western Ghats are an important step in safeguarding the persistence of MTT populations. Overall, our results demonstrate the use of citizen science data and its potential in modeling and understanding the geographic distribution and the calling phenology of an elusive, arboreal, and endemic amphibian species.