Regulation of xylanase production in two thermophilic fungi Scytalidium thermophilum and Sporotrichum thermophile was investigated. The expression of xylanase was found to be inducible in both the cases. Various carbon sources were tested so as to identify the inducers. Soy flour and oat spelt xylan induced maximum level of xylanase in Scytalidium thermophilum and Sporotrichum thermophile respectively. Induction of xylanase in Scytalidium thermophilum led to simultaneous induction of cellulase. The zymography of enzyme preparations revealed that different carbon sources caused differential expression of multiple isoforms of xylanase in Scytalidium thermophilum, but same isoforms were expressed by Sporotrichum thermophile irrespective of the carbon source used.