The phylogeny of the Synurophyceae was investigated by parsimony analysis of scale case characters and small-subunit (18S) ribosomal RNA (rRNA) sequence data. Analysis of 1 eustigmatophycean (outgroup), 3 chrysophycean, and 10 synurophycean 18S rRNA sequences corroborated the inference from ultrastructural information that the Synurophyceae is a monophyletic assemblage Tessellaria volvocina, which had been tentatively proposed as a member of the Synurophyceae, was confirmed as the earliest lineage within the Synurophyceae by both the molecular analysis and an evaluation of published ultrastructural data. A second set of analyses investigated the relationships among Tessellaria volvocina, 6 Synura species, and 10 Mallomonas species/varieties, with particular reference to the validity of current classifications of the Synurophyceae and the characters upon which they are based. The molecular and scale case phylogenies were not totally resolved but were largely congruent. The data sets were combined to produce another phylogeny, which showed greater resolution. The combined phylogeny weakly supported our representatives of Synura and Mallomonas as monophyletic groupings and also upheld several of the sections within these genera that are recognized by current classifications. However, some changes to the classification and delineation of these genera are recommended and predicted. Both our 18S rRNA sequence and scab case data sets were more appropriate for examining the branching order among the more closely related taxa rather than resolving the deeper branching points of the synurophycean phylogeny.