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Westiellopsis prolifica, a true-branching cyanobacterium isolated from the hyperarid desert soil habitats of El-Farafra Oasis (Western Desert of Egypt), was investigated with a polyphasic approach. The main morphological characteristics of our material, together with its habitat properties, corresponded (with minor discrepancies in the dimensions) to descriptions in the literature. On the basis of molecular data of the 16S ribosomal RNA gene, the strain of W. prolifica isolated from the El-Farafra Oasis clustered with available isolates of Westiellopsis and other genera of Hapalosiphonaceae. Bio-organic screening showed the presence of thylakoid lipids characterized by low unsaturation index and short fatty acyl chains, features presumably ensuring membrane functionality at high temperatures. Carotenoid and xanthophyll composition were typical of cyanobacteria (alpha/beta carotene 38.1%, echinenone 14.3%, zeaxanthin 13.4%, and myxoxanthophyll 8.8%). This study improved the knowledge on the distribution, autecology, phylogenetic position, and bio-organic characteristics of W. prolifica. Moreover, it confirmed that polyphasic studies of cyanobacteria are not only an important prerequisite for species delineation, but are also useful in characterizing ecophysiological adaptive mechanisms to special habitats.