This paper describes a new gas chromatographic method for the compositional analysis of algal galactans containing 3,6-anhydrogalactose, which is readily destroyed in usual acid hydrolysis and methanolysis. Mercaptolysis of galactans was carried out under an anhydrous condition using the newly developed solvent system, an ethanethiolic HCl solution which had been prepared by blowing dry HCl gas into ethanethiol. By heating galactans in 0.5 N HCl/ethanethiol at 60°C for 12 h, component sugars including 3,6-anhydrogalactose were released quantitatively as their diethyl mercaptals. The monosaccharide diethyl mercaptals were trimethylsilylated and analyzed by gas–liquid chromatography. Each component monosaccharide was detected as a single peak since neither anomeric nor structural isomers can be produced by mercaptolysis. Furthermore, the solvent system was improved by the addition of methanol in a ratio (2/1, v/v) of ethanethiol to methanol. Heating of galactans at 60°C in 0.5 N HCl/[ethanethiol:methanol (2/1, v/v)] released more rapidly and quantitatively monosaccharide diethyl mercaptals without any formation of monosaccharide methyl glycosides. The present method was applicable to not only algal galactans but also algal powders.