The Xanthophyceae have traditionally been classified using a phenetic classification system based upon vegetative cell structure. Species belonging to the class are placed in one of six orders corresponding to amoeboid, coccoid, filamentous, flagellate, palmelloid, or siphonous organization. Nuclear 18S rRNA gene sequences were determined for 29 species and aligned with 10 previously determined sequences. Parsimony and maximum likelihood trees inferred from these data imply that the orders Mischococcales (coccoid), Tribonematales (filamentous), and Vaucheriales (siphonous) are not monophyletic. The majority of species are divided between two clades defined by the presence or absence of a bipartite cell wall. Also, several families, particularly those placed in the Mischococcales, are resolved as polyphyletic. Results indicate that coccoid and filamentous life forms may have arisen independently at least three times, and some coccoid and filamentous life forms are resolved as closely related. For example, Heterococcus (filamentous) is more closely related to Mischococcus and Pseudopleurochloris (coccoid) than it is to other members of the Tribonematales. Our data strongly support the contention that Bumilleriopsis and Pseudobumilleriopsis are congeneric with Bumilleria. The siphonous xanthophytes including Asterosiphon, Botrydium, and Vaucheria probably do not form a monophyletic group although robust bootstrap support for this conclusion is low. Our results indicate that the generic, familial, and ordinal classification of the Xanthophyceae requires major revision.

Key words: algae, Mischococcales, systematics, Tribonematales, Vaucheriales, Xanthophyceae