Amphibians are facing extinctions worldwide as a result of numerous factors. Habitat alteration has long been implicated in the loss of biodiversity; however, we still do not know how different animal assemblages respond to habitat alteration. To investigate the impacts of anthropogenic habitat alteration on diversity, we studied amphibian assemblages across different habitats in the Chocó rainforest of northwest Ecuador. Amphibian diversity was estimated using intensive surveys along transects in primary and altered (historically logged) forest and riparian habitats, as well as along roads with varying levels of ongoing human activity. Our results suggest an interaction between habitat type and alteration on the diversity and composition of amphibian assemblages. Amphibian assemblages along rivers were the richest as well as the least impacted by habitat alteration. In addition, riparian zones harbored amphibian assemblages distinct from other habitat types, including rare and endangered species. Diversity and species richness were lower in secondary than in primary forest, suggesting that amphibian assemblages in interior forest habitat may be more vulnerable to alterations caused by logging. These findings suggest that amphibian assemblages in different habitat types (i.e., riparian vs. interior forest) may vary in vulnerability to habitat alteration. We discuss these findings in relation to land management plans that promote amphibian diversity in northwest Ecuador and recognize a good potential indicator species, Oophaga sylvatica, for identifying pristine habitat.