Nucleotide sequences of the nuclear-encoded small subunit (18S rDNA) and partial large subunit (28S rDNA) ribosomal DNA were determined in 30 different species of the haptophyte genera Prymnesium, Chrysocampanula, Chrysochromulina, Imantonia and Platychrysis, all belonging to the order Prymnesiales. Phylogenies based on these and other available haptophyte 18S, 28S and plastid 16S rDNA sequences were reconstructed, and compared with available morphological and ultrastructural data. The rDNA phylogenies indicate that the genus Chrysochromulina is paraphyletic and is divided into two major clades. This is supported by ultrastructural and morphological data. There is a major split between Chrysochromulina species with a saddle-shaped cell form (clade B2) and the remaining species in the genus (clade B1). Clade B2 includes the type species C. parva and taxa belonging to this clade thus retain the name Chrysochromulina. The non-saddle-shaped Chrysochromulina species analysed are closely related to Hyalolithus, Prymnesium and Platychrysis species. Imantonia species are sister taxa to these species within clade B1. An amendment to the classification of the order Prymnesiales and the genera Prymnesium, Platychrysis and Chrysochromulina is proposed with one new and one emended family (Chrysochromulinaceae and Prymnesiaceae, respectively), two new genera (Haptolina and Pseudohaptolina), and one new species (Pseudohaptolina arctica). We suggest a revision of the taxonomy of the Prymnesiales that is in accordance with available molecular evidence and supported by morphological data.