Two xylanases, MFX I and MFX II, from the thermophilic fungus Malbranchea flava MTCC 4889 with molecular masses of 25.2 and 30kDa and pIs of 4.5 and 3.7, respectively were purified to homogeneity. The xylanases were optimally active at pH 9.0 and at 60 degrees C, exhibited a half-life of 4h at 60 degrees C, and showed distinct mode of action and product profiles when applied to birchwood, oat spelt, and larchwood xylan, and to wheat and rye arabinoxylan. The xylanases were most active on larchwood xylan with K(m) values of 1.25 and 3.7mg/ml. K(cat)/K(m) values suggested that the xylanases preferentially hydrolyzed rye arabinoxylan. LC-MS/MS (liquid chromatography/mass spectrometry) analysis of tryptic digests of MFX I and MFX II revealed similarity with known fungal xylanases and suggests that that they belonged to the GH 11 and 10 glycosyl hydrolase super families, respectively. These xylanases can potentially be used in enzyme-assisted bleaching of the pulp derived from agro-residues, as well as production of xylooligosaccharides for pre-biotic functional food applications.