Although it is widely accepted that the plastids of plants and algae originated as endosymbionts, the details of this evolutionary process are unclear. It has been proposed that in organisms whose plastids are surrounded by more than two membranes, the endosymbiont was a eukaryotic alga rather than a photosynthetic prokaryote. The DNA-containing nucleomorph of cryptomonad algae appears to be the vestigial nucleus of such an algal endosymbiont. Eukaryotic-type ribosomal RNA sequences have been localized to a nucleolus-like structure in the nucleomorph. In support of the hypothesis that cryptomonads are evolutionary chimaeras of two distinct eukaryotic cells, we show here that Cryptomonas phi contains two phylogenetically separate, nuclear-type small-subunit rRNA genes, both of which are transcriptionally active. We incorporate our rRNA sequence data into phylogenetic trees, from which we infer the evolutionary ancestry of the host and symbiont components of Cryptomonas phi. Such trees do not support the thesis that chromophyte algae evolved directly from a cryptomonad-like ancestor.