A phylogeny of 21 haptophyte algae was inferred by maximum parsimony, neighbor-joining, and maximum likelihood analyses of sequences of the plastid-encoded gene, rbcL. Sequence variation in the spacer region of the RUBISCO operon was also investigated. In all the rbcL trees constructed, the haptophytes form two distinct clades: one includes the Pavlovales and the other includes the Prymnesiales, Coccosphaerales, and Isochrysidales (all sensuParke and Green 1976. This relationship coincides with the recent taxonomic treatment splitting the division into two subclasses, the Prymnesidae and Pavlovidae (Cavalier-Smith 1989) or the Prymnesiophycidae and the Pavlovophycidae using botanical suffixes ( Jordan and Green 1994), or into two classes, the Patelliferea and the Pavlovea (Cavalier-Smith 1993). In the Prymnesiophycidae, all the coccolithophorids examined are placed in a single clade, which suggests a single origin of the coccolithophorids and the ability of coccolith formation in the haptophytes. The genus Chrysochromulina is polyphyletic. Species of Chrysochromulina with a very long haptonema and a compressed cell body (typical of species including the type C. parva Lackey) form a clade, including Imantonia, that is often classified in the Isochrysidales in the neighbor-joining tree, whereas some species possessing a nontypical cell body and cell covering form a clade with Prymnesium and Platychrysis in all trees. It is suggested that loss of the haptonema in Imantonia and the reduction in Prymnesium and Platychrysis occurred secondarily and independently in two different lineages. Within the coccolithophorids, four clades are recognized: Pleurochrysis, Calyptrosphaera-Cruciplacolithus-Calcidiscus-Umbilicosphaera, Helicosphaera, and Emiliania-Gephyrocapsa. A non-coccolith-bearing haptophyte, Isochrysis, is an ingroup of the Emiliania-Gephyrocapsa clade, suggesting its secondary loss of the ability to form a coccolith. Sequence comparison of the spacer region of RUBISCO operon supports most results obtained in the analysis of rbcL sequences. Monophyly of the Prymnesiales sensu Parke and Green is still unclear because of low (<50%) bootstrap support for this group.