A phylogeny of marine Rhodophyta has been inferred by a number of methods from nucleotide sequences of nuclear genes encoding small subunit rRNA from 39 species in 15 orders. Sequence divergences are relatively large, especially among bangiophytes and even among congeners in this group. Subclass Bangiophycidae appears polyphyletic, encompassing at least three lineages, with Porphyridiales distributed between two of these. Subclass Florideophycidae is monophyletic, with Hlldenbrandiales, Corallinales, Ahnfeltiales, and a close association of Nemaliales, Acrochaetiales, and Palmariales forming the four deepest branches. Ceramiales may represent a convergence of vegetative and reproductive morphologies, as family Ceramiaceae is at best weakly related to the rest of the order, and one of its members appears to be allied to Gelidiales. Except for Gigartinales, for which more data are required, the other florideophyte orders appear distinct and taxonomically justified. A good correlation was observed with taxonomy based on pit-plug ultrastructure. Tests under maximumlikelihood and parsimony of alternative phylogenies based on structure and chemistry refuted suggestions that Acrochaetiales is the most primitive florideophyte order and that Gelidiales and Hildenbrandiales are sister groups.The Rhodophyta is a large, morphologically diverse assemblage of eukaryotes, with 2500-6000 species in about 680 genera (1). Although the division as a whole is well delimited (1, 2), its taxonomy at the levels of subclass and order has been unstable. Traditionally, two subclasses have been recognized, Bangiophycidae and Florideophycidae, with four and 14 orders, respectively. Recently, the former has been adjudged untenable (3-5) because it is not distinguished by synapomorphic characters. Alternatively, three new subclasses have been proposed to replace the Bangiophycidae and Florideophycidae on the basis of the degree of cellular transformation into spores (6). At the ordinal level (7), six new orders have been described since 1978 (8-12), and the large classical order Cryptonemiales has been subsumed into the similarly large Gigartinales (13), creating a heterogeneous assemblage of families that requires further resolution. Ordinal changes have arisen mainly from increasing appreciation of the significance of life-history variations and ultrastructure (5, 7, 9). However, taxonomic instability in Rhodophyta has also been ascribed to a lack of association with phylogenetic hypotheses, and attempts have been made (4, 6, 7) to infer phylogenetic relationships from morphological, anatomical, ultrastructural, life history, and chemical characters. Molecular sequences, particularly of nuclear genes encoding small subunit rRNA (SSU rDNAs) have proven useful in resolving phylogenetic relationships within other problematic groups (14-16 DNA Methods. DNA was extracted (18), and SSU rDNAs were amplified by using eukaryote-specific primers (19) as described (20). Amplification products were cloned into pUC and sequenced fully on both s...