A new desmid microalga species, Cosmarium yassinii A.A. Saber, El-Sheekh, Kouwets et Cantonati sp. nov., was isolated from two hyper-arid mountain valleys, so-called “wadis”, in the Eastern Desert of Egypt. The distinctive morphological features of this new species were established using light and scanning electron microscopy observations, and also by documenting its life-cycle stages. Taxonomically, C. yassinii is characterized by a cell wall sculpture consisting of isolated granules or small warts arranged circularly in the swollen mid-region of each semicell, never forming parallel vertical ridges or costae as in morphologically similar species, and the interesting shape of the marginal granules appears as small emarginate “combs” or crenae, including its knobby zygospores. Similarities and differences with the morphologically most closely related species are discussed in detail. Ecologically, C. yassinii seems to prefer alkaline freshwater environments with lower nutrient concentrations and a NaCl/HCO₃ water type. The detailed assessment and documentation of the biodiversity of these peculiar freshwater ecosystems are a fundamental prerequisite to adequately inform their protection strategies.