The articulated coralline Calliarthron cheilosporioides Manza produces segmented fronds composed of calcified segments (intergenicula) separated by uncalcified joints (genicula), which allow fronds to bend and reorient under breaking waves in the wave-swept intertidal zone. Genicula are formed when calcified cells decalcify and restructure to create flexible tissue. The present study has identified important differences in the main agaran disaccharidic repeating units [→3)-β-d-Galp (1→ 4)-α-l-Galp(1→] synthesized by genicular and intergenicular segments. Based on chemical and spectroscopical analyses, we report that genicular cells from C. cheilosporioides biosynthesize a highly methoxylated galactan at C-6 position with low levels of branching with xylose side stubs on C-6 of the [→3)-β-d-Galp (1→] units, whereas intergenicular segments produce xylogalactans with high levels of xylose and low levels of 6-O-methyl β-d-Gal units. These data suggest that, during genicular development, xylosyl branched, 3-linked β-d-Galp units present in the xylogalactan backbones from intergenicular walls are mostly replaced by 6-O-methyl-d-galactose units. We speculate that this structural shift is a consequence of a putative and specific methoxyl transferase that blocks the xylosylation on C-6 of the 3-linked β-d-Galp units. Changes in galactan substitutions may contribute to the distinct mechanical properties of genicula and may lend insight into the calcification process in coralline algae.