Fuel ethanol that is renewable energy was demanded in the future. It was better if we could utilize agricultural wastes (straws and bagasse) as sources for ethanol production. These biomass sources were developed by enzymes such as xylanase. This enzyme could break the plant cell wall down into xylan. Then xylan was saccharified hydrosylate as xylose that could be fermented to ethanol by yeast. Thus, we interested to isolate xylanase producing Thermomyes lanuginosus. Our result showed that isolated T. lanuginosus separated to 2 groups depending on their xylose induced xylanase formation. Moreover, it was found a group of strains produced high xylanase either in the xylan or xylose medium. Addition of xylose to the xylan medium did not decrease xylanase production by T. lanuginosus THKU-11 and THKU-25 that were members of this group. In contrast, there was another group producing high xylanase only in the xylan medium. Addition of xylose to the xylan medium resulted decreasing of xylanase formation in T. lanuginosus TISTR 3465 and THKU-85 that were belonged to this group. Phylogenetic analysis obtained from random amplified polymorphic DNA (RAPD) pattern using one primer UBC 241 point to greater diversity of high and low xylanase producing strains using xylose as a carbon source.