Phylogenetic trees among eukaryotic kingdoms were inferred for large- and small-subunit rRNAs by using a maximum-likelihood method developed by Felsenstein. Although Felsenstein's method assumes equal evolutionary rates for transitions and transversions, this is apparently not the case for these data. Therefore, only transversion-type substitutions were taken into account. The molecules used were large-subunit rRNAs from Xenopus laevis (Animalia), rice (Plantae), Saccharomyces cerevisiae (Fungi), Dictyostelium discoideum (Protista), and Physarum polycephalum (Protista); and small-subunit rRNAs from maize (Plantae), S. cerevisiae, X. laevis, rat (Animalia), and D. discoideum. Only conservative regions of the nucleotide sequences were considered for this study. In the maximum-likelihood trees for both large- and small-subunit rRNAs, Animalia and Fungi were the most closely related eukaryotic kingdoms, and Plantae is the next most closely related kingdom, although other branching orders among Plantae, Animalia, and Fungi were not excluded by this work. These three eukaryotic kingdoms apparently shared a common ancestor after the divergence of the two species of Protista, D. discoideum and P. polycephalum. These two species of Protista do not form a clade, and P. polycephalum diverged first and D. discoideum second from the line leading to the common ancestor of Plantae, Animalia, and Fungi. The sequence data indicate that a drastic change occurred in the nucleotide sequences of rRNAs during the evolutionary separation between prokaryote and eukaryote.