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Alice’s Wrinkled Frog (Nyctibatrachus aliciae) is an endemic anuran amphibian of the Western Ghats. The population estimation of this species in native forest and adjoining secondary forest has revealed distinct differences in size. The population size in native forest (n = 554) was large compared to secondary forest (n = 234). The two forest habitats are characterised by air temperature, humidity, light intensity and canopy cover differences. Manmade activity and habitat variables likely influenced the reduction of population size in secondary forest.