An interesting population of ulvacean green algae was collected from a limno-rheocrenic, thermal, mineral (chloride, sodium, sulphate) spring known as "Ain Abu Sherouf" in the Siwa Oasis, the Western Desert of Egypt. A detailed combined investigation on its morphotaxonomy, autecology, and a multilocus sequence data set including the chloroplast-encoded rbcL gene and the nuclear-encoded nrDNA SSU and ITS allowed us to identify this population as Ulva flexuosa subsp. paradoxa (syn. Ulva paradoxa, Ulvales, Chlorophyta), although the algal thalli were in average narrower than usual in this taxon. Analysis of the molecular rbcL-ITS sequencing data demonstrated a close phylogenetic relationship of the studied population to two Ulva isolates from Japan and China and their taxonomic status was further discussed. The pigment profiling confirmed chlorophylls and carotenoids typical of the Ulvaceae (lutein, α/β-carotenes, violaxanthin, and neoxanthin). Lipidomic analysis revealed the presence of the monogalactosyl diacylglycerols (MGDG), digalactosyl diacylglycerols (DGDG), sulfoquinovosyl diacylglycerols (SQDG), and diacylglyceryl N,N,N-trimethylhomoserine (DGTS) lipid classes. Presence of the plasma membrane DGTS lipids in remarkable proportion might be an adaptation to this nutrient-poor mineral spring habitat, with relatively low phosphorus values. The lower unsaturation index (UI) values of the plastidial DGDG and SQDG lipids are likely to reflect the need to maintain adequate membrane fluidity in this thermal mineral spring system. This polyphasic study not only extended our little knowledge on the distribution, autecology, and adaptive mechanisms of U. flexuosa subsp. paradoxa in the Saharan habitats of Africa, but also reassessed and refined the taxonomic and phylogenetic affiliation of previously sampled close relatives from East Asia.