The impact of genetic and fruit ripening on hemicelluloses fine structure was studied in twelve near isogenic lines of tomato fruits harboring firmness QTL. The sugar composition and the MALDI-TOF MS oligosaccharides profile after glucanase hydrolysis of the cell walls were determined from all green and red fruits pericarp tissue. MS profiles showed two major series of oligomers attributed to xyloglucan (XG) and glucomannan (GM) with minor peaks for xylan and ions attributed to galacto-oligomers. The oligosaccharides MS intensity varied significantly with the fruit genetic and ripening status. Correlations between MS intensity indicated structural regulations of both XG and GM structures with genetics and ripening. These results point to a region on the tomato chromosome 9 controlling cell wall galactose metabolism.