Sandy Gypsiferous soils are among the major soils of arid regions of the world. In the Sahara desert, they occupy large areas, where gypsum accumulations are favoured by the polyextreme environment. Various complex gypsic pedofeatures have been recognized and each hosts a striking biological diversity of photoautotrophic communities including Biological soil crusts (Biocrusts). But little is known concerning soil microfabrics related to the interactions between Biocrusts and mineral constituents. In this study, we report the micromorphological approach of the soil microhabitats of endolithic and epilithic Biocrusts growing in some sandy Gypsiferous soils in the Sahara desert. Biocrusts were studied at four sites in high plateau and low Sahara, Algeria. We sampled topsoil at each site from a sandy gypsic or petrogypsic horizon containing active Biocrusts. Thin sections were made on undisturbed and impregnated topsoil samples, they were studied with a polarizing microscope. Additional soil aggregates were selected for ultramicroscopic observations. The results showed that: i) Biocrusts of the high plateau are mainly composed of epilithic mosses. The distribution of aeolian dust, sand and carbonated silt particles were embedded in a Biocrust organic material stabilizing soil matrix. ii) Endolithic Biocrusts of the low Sahara are strongly associated with gypsic crystalline pedofeatures. Gypsum crystals and crystal intergrowths are aggrading together with sparite and micro-sparite calcite. The common organic pedofeatures observed include organic residues, commonly derived from micro-photoautotrophs (green algae and cyanobacteria), they are often observed as infilling in the inter-crystals porosity. SEM observations show the presence of bio-filamentous materials and cells with a chain structure. Amorphous fine organic material is identified in the interface calcite/gypsum crystals, it seems to be related to the CO2 pressure and geochemical dynamic (dissolution/precipitation) of these minerals. Some endolithic Biocrusts exhibit a well-developed microstructure and porosity within large gypsum crystals, this microstructure was mainly caused by bioturbation.