Amphibians are declining worldwide. At the same time, each year many species of amphibians are described, indicating that biological diversity on Earth remains poorly understood. This is especially true for mountainous regions, such as the Himalayas, which are also regarded as a biodiversity hotspot. However, it is most likely that the current diversity of amphibians in Nepal is highly underestimated. Amphibian inventories by the past researchers primarily used phenotypic characters as the basis for species identification. However, the application of molecular systematics methods to taxonomic studies has successfully uncovered the taxonomic status of several cryptic taxa. This study used both molecular (16S rDNA sequences) and morphological comparisons and estimated the diversity of amphibians from Nepal. This study reports the occurrence of 38 species of amphibians based on both molecular and morphological comparisons. Among them, three species were recorded for the first time in Nepal. This study also invalids the taxonomic status of Sphaerotheca paschima. This study highlights the importance of integrative taxonomic approaches that help to resolve the current taxonomic ambiguities of Nepalese amphibians.