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Abstract Background Little is known about phytoplankton communities inhabiting low pH environments such as volcanic and geothermal sites or acidic waters. Only specialised organisms are able to tolerate such extreme conditions. There is, thus, low species diversity. We have characterised the previously isolated acid tolerant <it>Chlorella</it>-like microalgae <it>Viridiella fridericiana</it> and <it>Chlorella protothecoides</it> var. <it>acidicola</it> by microscopical and biomolecular methods in order to assess their phylogenetic relationships. Results Both isolates belong to the trebouxiophycean lineage of chlorophytes. 18S and ITS1 sequence data clearly confirm that <it>Viridiella fridericiana</it> constitutes a new genus apart from the morphologically similar and likewise acid tolerant microalga <it>Chlorella saccharophila</it>. <it>Chlorella protothecoides</it> var. <it>acidicola</it> on the other hand is not a variety of <it>Chlorella protothecoides</it> but falls within a heterogeneous cluster consisting of <it>Nannochloris</it>, "<it>Chlorella</it>" spec. Yanaqocha, and <it>Koliella,</it> and is most closely related to algae which were also isolated from extreme environments. Conclusions The distribution of acid tolerant strains in the 18S rRNA tree shows that acquisition of acid tolerance was unlikely a monophyletic event in green microalgae. We propose that different strains have independently adapted to extreme environments. Some of them have spread worldwide and were able to colonise other extreme habitats. Considering the problems of successfully isolating acid tolerant strains, acidic soils could represent an unsuspected source of biological diversity with high potential for biotechnological utilisations.</p

Phylogenetic relationships and taxonomic position of Chlorella-like isolates from low pH environments (pH < 3.0).