The Andes Mountains of South America are considered one of the most biologically diverse and threatened areas in the world. Habitat destruction in this area is among the most common causes of amphibian population declines and extinction, but few studies have used complementary approaches to understand the interplay between habitat transformation and microhabitat use by amphibians. We studied the anuran diversity in modified vegetation cover types in a cloud forest in the tropical Andes of Colombia in order to compare components of biological diversity and microhabitat preferences among forested and human-altered habitats. Secondary Forest and Riparian Forest were the vegetation cover type with the highest local diversity, whereas the highest turnover was between the forested and human-altered areas. The species in the assemblage showed specific microhabitat associations with the substrate and the vertical stratification, with lower mean values of niche overlap between species pairs in forested area than in human altered areas. These results show how anthropic intervention creates less favorable vegetation cover types for some species of anurans and the way in which preferences for a specific micro-habitat could influence distribution in these vegetation cover type.