Purified extracellular endo‐1,4‐β‐xylanase (EC 3.2.1.8) of the yeast Cryptococcus albidus was found to catalyze not only the known 1,4‐β‐transfer, but an alternative transglycosylation reaction leading to the formation of 1,3‐β‐glycosidic linkages. From a mixture of products of β‐xylanase degradation of phenyl β‐D‐xylopyranoside three xylooligosaccharide fractions, differring chromatographically from the 1,4‐β‐linked products, were isolated by preparative paper chromatography. Their structure was elucidated by mass spectrometry, 13C‐NMR spectroscopy and enzymic hydrolysis by β‐xylanase and β‐xylosidase. The isomeric xylotriose was identified as 3‐O‐β‐D‐xylopyranosyl‐4‐O‐β‐D‐xylopyranosyl‐D‐xylose. The fraction of isomeric tetrasaccharides was found to be represented mainly by 4‐O‐β‐D‐xylopyranosyl‐3‐O‐β‐D‐xylopyranosyl‐4‐O‐β‐D‐xylopyranosyl‐D‐xylose. The xylooligosaccharides containing one 1,3‐β‐linkage were also produced on the enzyme treatment of 1,4‐β‐xylotriose and 1,4‐β‐xylan. When treated with the enzyme responsible for their synthesis, the isomeric xylooligosaccharides were hydrolyzed at the 1,3‐β‐linkage, despite the fact the enzyme does not attack 1,3‐β‐xylan. The results are interpreted in the relation to the characterized four‐subsite substrate‐binding site of the enzyme.