ABSTRACT: The archaeal and bacterial 16S rRNA gene diversities of the Polihnitos (89°C), Edipsos (81.8°C), Thermopiles (38.9°C), Eleftheres (41.2°C) and Lagadas (35.2°C) geothermal springs in Greece were investigated. The abundance of prokaryotic cells varied between 0.02 × 10⁵ and 0.92 × 10⁵ cells ml^–1. A total of 227 archaeal and 501 bacterial clones were analysed, which were attributed to 85 and 121 operational taxonomic units (OTUs), respectively. Library clone coverage, based on Good’s C estimator, was satisfactory (>75%), except for the Archaea in Thermopiles (~40%) and Eleftheres (~60%). Most of the archaeal phylotypes were related to sequences of yet-uncultivated microorganisms retrieved from terrestrial geothermal springs, deep-sea hydrothermal vents and the subsurface. A much higher number of bacterial phylotypes was related to cultivated microorganisms from similar environments. The thermophilic nature of most of the discovered phylotypes was also supported by their high G+C content, which was positively correlated with the springs’ temperatures. The springs showed different diversity patterns for Bacteria and Archaea, with Bacteria having higher diversity only in Polihnitos and Lagadas springs. The Shannon diversity index H’ showed larger variation for Archaea (0.23 to 3.44) than for Bacteria (1.22 to 3.03) and was unrelated to the prevailing temperature, pH, salinity and dissolved oxygen content. Archaeal and bacterial clone libraries respectively contained 50 to 94.1 and 68.8 to 96.2% rare phylotypes (i.e. those that appear only once or twice in the clone library), indicating the importance of rare phylotypes in shaping community diversity.