To date, knowledge about the herpetological diversity and the species distribution in the Democratic Republic of the Congo remains largely incomplete. In order to fill this gap, we carried out long-term and large-scale herpetological surveys to improve the knowledge about the herpetofauna occurrence and species composition data. Site scanning, visual encounter, transect and quadrat methods were used along with call recordings for identifying and locating amphibians on each survey site. Additional data were gathered from literature reviews and museum collections. The herpetological diversity was assessed on twenty-eight survey sites located in both Congo Basin and Albertine Rift ecoregions. All surveyed localities and sites were georeferenced in order to generate distribution maps by using QGIS 2.14.0 software. Herpetological diversity indices were generated using the PAST software. Using morphological characters and information provided by DNA analysis, species lists were produced per site and on national level. The results show that the rich Congolese herpetofauna is composed of 605 species, including 247 (40.83%) amphibians and 358 (59.17%) reptiles. There are 57 endemic amphibian species (23.1%) and of these, 19 (32.7%) are located in Protected Areas. There are 38 endemic reptile species (10.6%) and of these, twelve (31.5%) are found in Protected Areas. Furthermore, there are nine and seventeen threatened amphibian and reptile species respectively; but only 20% of these have been detected inside of national parks. Concerning this situation, it appears that, if no action is undertaken for fighting against the human pressure on habitat, there will be a decline in populations and species in the Democratic Republic of the Congo. Based on relevant indices, including species richness, rarity, diversity, endemism, and presence of threatened species, and other objective criteria in respect to international standards, the following ten sites were identified as sites of priority for conservation: Marungu, Kabobo, Itombwe, Ituri, Tshopo, Mai Ndombe Tumba, Lualaba, Lukaya, Sankuru, and Ubangi Uele. These sites are proposed as new Protected Areas for reaching the government's national conservation targets of land preservation necessary for conserving the rich biodiversity.