The stress-70 protein family has previously been shown to be a useful tool for molecular phylogeny at the kingdom to family levels. Although sequences of many members of the stress-70 family are available, few genes from the Protoctista have been sequenced to date. Phylogenetic analyses of algae based on various molecules have not, as yet, provided clear results concerning relationships between major divisions. We cloned and sequenced several algal stress-70 genes in order to provide additional data and to further analyse phylogenetic relationships among algal divisions. New nuclear sequences were obtained from Guillardia theta (Cryptophyta), Ascophyllum nodosum (Heterokontophyta) and Cyanophora paradoxa (Glaucocystophyta). Phylogenetic trees of the stress-70 protein family calculated using different methods are presented. In our trees, the heterokont alga Ascophyllum nodosum is closely related to the slime mould Dictyostelium discoideum, while the nucleomorph (eukaryotic endosymbiont) of the cryptophyte Rhodomonas salina seems to be related to the chlorobiont lineage. The glaucocystophyte Cyanophora paradoxa and the nuclear sequence (host) of the cryptomonad alga Guillardia theta also seem to be closely related. The Cryptophyta and the heterokont algae have evolved from different secondary endosymbiotic events involving different hosts and probably different endosymbionts. However, until more stress-70 sequences of algal divisions become available no definitive conclusions can be drawn concerning branching of the major divisions.