This study reports the regulation of multiple xylanases produced by Myceliophthora sp. IMI 387099. Fructose was found to positively regulate the expression of multiple xylanase when used as sole carbon source. The xylanases (EX1 and EX2) of acidic pI were expressed in the presence of simple sugars (glucose, arabinose, and xylose), whereas xylanase of both acidic as well as basic pI (EX1, EX2, EX3, and EX5) were expressed in the presence of fructose, xylan, and combination of xylan and alcohol. The combination of fructose and xylan also led to expression of an additional xylanase (EX4). The positional isomer (iso-X4) was found to be the key transglycosylation product when cultures were grown in the presence of fructose and xylan. In the presence of alcohols, the higher expression of xylanase was ascribed to the synergistic effect of alkyl glycoside and other transglycosylation products present in the culture extracts.