The only eukaryotes found in highly acidic environments (pH 0.5-3) with ele
vated temperatures (up to 56 degreesC) are three species of unicellular red
algae: Cyanidioschyzon merolae, Cyanidium caldarium and Galdieria sulphura
ria. These habitats are scattered all over the world and are usually very s
mall. Because all three species are strictly acidophilic and will not toler
ate desiccation, distribution by wind or water seems very unlikely. The pop
ulations in the various habitats might have been isolated for very long tim
es, providing a unique opportunity to observe a significant degree of indep
endent evolution under strong, selective pressure. We investigated the biog
eography of 18 isolates of these red algae by comparison of partial sequenc
es of the 18S rRNA. A gene tree based on ISS rRNA assigns 15 strains to one
branch with high bootstrap values. These isolates share the feature of fac
ultative heterotrophy, whether or not they were originally placed in the ge
nus Galdieria. The remaining three strains - Galdieria maxima, C. merolae a
nd 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 evo
lutionary 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 eukaryoti
c organisms the limits of phylogenetic analysis may be reached.