A water sample was obtained from an arheic oasis in the deep Sahara Desert, the Gueltates Afilal in Tamanrasset (Algeria). Five diatom strains were isolated, cultivated and identified as Tryblionella apiculata, Nitzschia supralitorea, Fistulifera saprophila, Navicula veneta and Thalassiosira pseudonana using a combination of scanning electron microscopy and next generation sequencing. The diatoms identified are opportunistic and cosmopolitan species with known tolerances to organic pollution and variations in salinities, often found in meso- and polysaprobic zones in Europe. Their complete organellar genomes have been sequenced and some exhibit features never observed among diatoms before. To our knowledge this is the first time that living specimens of diatoms from the deep Sahara are identified using modern taxonomical tools in the frame of a study which also demonstrates the possibility to cultivate such material in laboratories for further experiments on biogeography and bioindication. Our study also suggests that European identification keys can be effective when employed on diatoms from the Sahara.