Abstract. The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 16S rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress.Cyanobacteria are ancient oxygenic and photosynthetic prokaryotes that have been found in the fossil record dating back 3.5 billion years. During cyanobacterial evolutionary history, the ancient prokaryotes have established themselves in diverse aquatic and terrestrial habitats, exhibiting wide ranges in temperature, salinity, water potential, pH, and irradiance [38]. Cyanobacteria provide an excellent system for testing hypotheses about the evolution of tolerance.The heterocystous filamentous cyanobacterial genus Nostoc, known as one of the most widespread phototrophic taxa, is common in both terrestrial and aquatic habitats [5,17]. Much of the success of Nostoc in terrestrial habitats is relative to its ability to remain desiccated for months or years and to recover metabolic activity within hours to days after rehydration. Nostoc cells experience extremes of desiccation, of which the water content is 0.02 to 0.05 g water cell solid -1 , approximately one order of magnitude lower than that of eubacterial spores (0.21 to 0.58) [27]. The mechanisms involved in the desiccation tolerance of Nostoc have been investigated using ecophysiology, biochemistry, and molecular biology [13,30,31,36]. However, the stability and biophysical properties of macromolecules inside desiccated cells are still poorly understood. Even though modifications of genome DNA, such as hypermethylation, have been observed in old desiccated sample of Nostoc species [15,31], it is unclear what effects these modifications have on the fitness of the desiccated cells.The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product and a suitable fitness indicator in evolutionary studies [4,18,29]. Because ribosomal RNA molecules create the structural framework for the ribosome, the sequences represent not only genotypes but also structural phenotypes. In addition, rRNA can serve as a ribozyme in peptide-bond synthesis [23]. These characteristics can be used in the test of the evolutionary ecolo...