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The treatment of straws from different plants for a long time up to 60 days could lead to an enrichment of organisms which have xylanases with high pH optima. The isolated fungi from ammonia treated-rice staw and sugar cane bagasse recorded 366 colonies constituting 10 species, while sugar can bagasse isolates reached 215 colonies representing 7 species. Sugar can bagasse as an isolation source possessed higher fungal diversity than rice straw. Mesophilic fungi were dominant in either rice staw or sugar can bagasse sources followed by the thermophilic fungi, which were isolated rarely. Scopulariopsis brevicaulis highly dominated straw and bagasse. Thermophilic Aspergillus versicolor and mesophilic Scopulariopsis brumptii dominated bagasse, whereas thermophilic Aspergillus terreus and mesophilic Acremonium strictum were encountered from straw.