A phylogenetic analysis was conducted on 21 biraphid naviculoid diatom species (from three orders and five families, using 5 protoplast and 21 frustule characters) to test whether the recently described genus Craspedostauros was more closely related to members of the Mastogloiaceae or to other stauros-bearing diatoms. The analysis also tested, and confirmed, the hypothesis that the stauros, as recognized by light microscopy, is a homoplastic character. Whereas partitioned analyses of protoplast and frustule data resolved different parts of the ‘total’ tree, using NONA parsimony analysis of all the data, one tree was obtained. This tree placed Craspedostauros in the mastogloialean clade, rather than near Stauroneis, Staurophora, Haslea or Meuniera. The ordinal and familial groupings suggested by Round and others were also confirmed by the analysis, supported particularly by protoplast and some ultrastructural features.