The partial sequences of the 18S rRNA gene and the rbcL gene, RuBisCo spacer region of representatives of the Dictyotaceae were determined and compared to resolve their phylogenetic relationships. A total of 1,861 base pairs of 18S rDNA sequences were aligned and examined. There was a high similarity of nucleotide sequences within the tribe Dictyoteae (99.4–99.6%) and the tribe Zonarieae (92.8–99.8%). The largest intergeneric divergence within the Dictyotaceae was 7.31%, between Dilophus and Zonaria. The aligned 422 bases of partial rbcL gene sequences gave a similar phylogenetic relationship among taxa to those of the 18S rDNA sequences, although our alignment covered less than 30% of the whole gene. All genera of Dictyotales consisted of several clades forming a polychotomy in MP trees based on partial rbcL gene sequences and on 18S rDNA sequences. The genera within the tribe Dictyoteae formed a clade, a Dictyota–Phacydictyon–Dilophus clade, while genera of the tribe Zonarieae formed four clades: Padina; Distromium–Lobophora–Zonaria;
Spatoglossum–Lobospira; and Dictyopteris–Spatoglossum. All genera of the Dictyotaceae included in these sequence analyses are classified into five groups, which have little phylogenetic resolution among them. The genera classified in the tribe Zonarieae according to Womersley's criteria do not appear to be monophyletic, based on our analyses. Although not all genera of Dictyotaceae were analysed, our data suggest that the status of the meristem cells should not be a criterion for separating tribes within the family Dictyotaceae and that other hierarchical systems should be adopted to properly reflect phylogenetic relationships.