Cryptomonad algae contain a photosynthetic, eukaryotic endosymbiont. The endosymbiont is much reduced but retains a small nucleus. DNA from this endosymbiont nucleus encodes rRNAs, and it is presumed that these rRNAs are incorporated into ribosomes. Surrounding the endosymbiont nucleus is a small volume of cytoplasm proposed to be the vestigial cytoplasm of the endosymbiont. If this compartment is indeed the endosymbiont's cytoplasm, it would be expected to contain ribosomes with components encoded by the endosymbiont nucleus. In this paper, we used in situ hybridization to localize rRNAs encoded by the endosymbiont nucleus of the cryptomonad alga, Cryptomonas phi. Transcripts of the endosymbiont rRNA gene were observed within the endosymbiont nucleus, and in the compartment thought to represent the endosymbiont's cytoplasm. These results indicate that the endosymbiont produces its own set of cytoplasmic translation machinery. We also localized transcripts of the host nucleus rRNA gene. These transcripts were found in the nucleolus of the host nucleus, and throughout the host cytoplasm, but never in the endosymbiont compartment. Our rRNA localizations indicate that the cryptomonad cell produces two different of sets of cytoplasmic-type ribosomes in two separate subcellular compartments. The results suggest that there is no exchange of rRNAs between these compartments. We also used the probe specific for the endosymbiont rRNA gene to identify chromosomes from the endosymbiont nucleus in pulsed field gel electrophoresis. Like other cryptomonads, the endosymbiont nucleus of Cryptomonas phi contains three small chromosomes.