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Desertifilum is a filamentous cyanobacterium of crusts and biofilms, recently described from the extreme hot and dry Thar Desert in north-western India. A new species was isolated from a warm spring near Lake Bogoria, Kenya and was characterised by light and electron microscopy and phylogenetically using the 16S rRNA gene, beta and alpha subunits including intergenic spacer (cpcBA-IGS) and 16S-23S internal transcribed spacer (ITS). The aquatic habitat of the new material from Kenya revealed a wider distribution of members of this genus. The new taxon was found to be closest to Desertifilum tharense (Oscillatoriales). The separation of the new species described here as D. fontinale sp. nov., using conventional and molecular traits, was based on differences in phenotypic features, 16S-23S ITS sequence and habitat.