Nucleotide gene sequences for both the nuclear-encoded small-subunit RNA (SSU) and plastid-encoded large subunit of RuBisCO (rbcL) were determined for 16 species classified in the red algal order Gelidiales. Sequence comparisons indicate that rbcL is evolving at a faster rate than SSU in these species and that there is a more even distribution of changes across the length of the rbcL gene compared with that observed for the SSU gene. The rbcL sequences also showed a marked anti-GC bias at synonymous third-codon base positions. Parsimony and maximum-likelihood analyses were used to generate phylogenetic trees from both separate and combined analyses of the two sequence data sets. Relationships among most taxa are resolved robustly; however, the relative order of branching for the Capreolia and Ptilophora clades remains uncertain. The molecular data provide unambiguous, independent support for recognition of the newly established genus Pterocladiella. Although the position of Pterocladiella within the Gelidiales was not resolved clearly by the rbcL data alone, analyses of both the SSU and combined data matrices indicate that this genus is one of the three earliest-diverging lineages within the order. These data also suggest that Gelidium as currently circumscribed is not monophyletic. Molecular and morphological evidence suggests that the origin and, perhaps, diversification of the major lineages of gelidialean algae is correlated with distinct, independently evolved nutritional strategies for the developing carposporophyte.