The research on amphibians and their conservation efforts have gained worldwide attention, since the group includes the highest number of threatened and data deficient species when compared with other vertebrates. However, amphibians have long been neglected in wildlife conservation, management decisions, policy making and research agendas in Pakistan.  In this paper, the annotated checklist of the 21 amphibian species of Pakistan, the key to their identification, and detailed discussions on the occurrence of variation in species including the genera Minervarya, and Sphaerotheca are provided. We found statistically significant difference in the morphometric measurements of males but non-significant difference in the females of the two forms (rusty dorsum and dotted dorsum) of S. maskeyi. Some genera, such as Microhyla, Uperodon, Minervarya, Allopaa, Chrysopaa, Euphlyctis, Nanorana and Sphaerotheca that are found in Pakistan need additional data to compare molecular taxonomy and detailed comparisons with those found in other South Asian countries. Predicaments in amphibian research in Pakistan are discussed, gaps identified, and suggestions have been made. Although the likelihood of occurrence of chytrid fungus in Pakistan is predicted to be low, the data deficiency merits studying the prevalence of the fungus, particularly in the northern regions of the country which exhibit complex and dynamic ecosystems. It is recommended to conduct systematic and coordinated surveys throughout the country to build a data base on species occurrence and distribution. Additionally, monitoring of wild populations, threat mitigation, and appropriate legislation are suggested as long term measures. By adopting an inclusive wildlife conservation approach in Pakistan, amphibians could be integrated into wildlife conservation and management efforts.