Six Leptolyngbya strains, isolated from the archaeological surfaces of hypogean sites, were phenotypically and genetically characterized by light and electron microscopy and 16S rRNA gene and 16S-23S internally transcribed spacer (ITS) sequencing. Three phycoerythrin-rich (red) and three phycocyanin-rich (green) isolates were assigned to different operational taxonomic units (OTUs). Among the green isolates, one strain showed an OTU intraspecific variation due to differences in the ITS sequences and genomic polymorphism. Within the ITS sequence, variable regions, conserved domains and tRNA Ile and tRNA Ala genes showed high sequence identity among the phylotypes. Together, these data indicated a relatedness of the six strains to other Leptolyngbya from subaerophytic and geothermal environments and allowed the definition of novel Leptolyngbya OTUs.Archaeological hypogea, such as Roman catacombs and the necropolis, are man-made underground sites illuminated from natural openings to the outside and/or from artificial lights that permit visits by tourists. The low-light conditions (photosynthetic photon flux density of Ͻ2 mol m Ϫ2 s Ϫ1