Schistosomiasis is an endemic parasitic disease currently infesting the sub-Sahara countries and has caused over 200 million infections worldwide. It is transmitted through water bodies and their intermediate host (IH), freshwater snails. By recording the geographical distribution and taxonomic information of the IH snails, a better understanding on the transmission pathway and proper execution on the disease prevention can be made accordingly. Thus, multiple excursions and sampling have been performed during 2012 and 2020 in several sub-Saharan African countries that are endemic for schistosomiasis by the Royal Museum for Central Africa, Belgium) and African partner institutes. Freshwater snail samples (with possible parasite infections) fixed on ethanol are here compiled in this dataset. The taxonomic identification was done mostly to genus-level due to the high morphological plasticity that exist among certain snail species. Yet, for many sample species-level ID was confirmed by DNA barcoding including Biomphalaria pfeifferi, Bulinus globosus, Bulinus truncatus, Bulinus forskalii, Radix natalensis, Pseudosuccinea columella, Physa acuta, Gyraulus connollyi, Melanoides tuberculata and others. We would like to thank all our collaborators (according to countries’ alphabetic order) for their significant contributions to this dataset: Dr. Felicité Teukeng (Faculty of Health Sciences University of Montagnes, Cameroon), Dr. Joule Madinga (Institut National de Recherche Biomédicale, DRCongo), Prof Patrick Mitachi Mulopo (Université de Kinshasa, DRCongo), Dr. Casim Umba Tolo (Pharm-Bio Technology and Traditional Medicine Centre (PHARMBIOTRAC), Mbarara University of Science & Technology, Uganda), Dr. Bruno SENGHOR, (Université Cheikh Anta Diop de Dakar, Senegal), Dr. Maxwell Barson and Tamuka Nhiwatiwa (Department of Biological Sciences, University of Zimbabwe, Zimbabwe).