The only eukaryotes found in highly acidic environments (pH 0·5–3) with elevated temperatures (up to 56 °C) are three species of unicellular red algae: Cyanidioschyzon merolae, Cyanidium caldarium and Galdieria sulphuraria. These habitats are scattered all over the world and are usually very small. Because all three species are strictly acidophilic and will not tolerate desiccation, distribution by wind or water seems very unlikely. The populations in the various habitats might have been isolated for very long times, providing a unique opportunity to observe a significant degree of independent evolution under strong selective pressure. We investigated the biogeography of 18 isolates of these red algae by comparison of partial sequences of the 18S rRNA. A gene tree based on 18S rRNA assigns 15 strains to one branch with high bootstrap values. These isolates share the feature of facultative heterotrophy, whether or not they were originally placed in the genus Galdieria. The remaining three strains – Galdieria maxima, C. merolae and C. caldarium – form a sister clade to this group. The exact position of these two groups in relation to other red algae remains unresolved. The evolutionary distance between individual Galdieria strains is high, indicating that within this genus several races have developed significantly altered 18S sequences. Our comparison of 18S sequences from thermo-acidophilic red algae indicates that even within a seemingly homogeneous group of eukaryotic organisms the limits of phylogenetic analysis may be reached.