This study aimed to assess the distribution and species occurrence of microscopic fungi isolated from two types of self-heating lignocelluloses: (1) sugarcane filter cakes (SFCs) and (2) sugarcane bagasses (SBGs). Three sugar mill refineries in Thailand were chosen: (1) the Eastern Sugar & Cane Co., Ltd. in Sa Kaeo Province (Site I); (2) the T. N. Sugar Industry Co., Ltd. in Lop Buri Province (Site II) and (3) the Buri Ram Sugar Factory Co., Ltd. in Buri Ram Province (Site III). We isolated 79 isolates, which represented 23 species in 11 genera. EightAspergillus species (37.78% of all species) were identified; this genus corresponded to the predominant mycoflora. Our results indicated that the most frequently encountered taxa, which represented either the most dominant fungi or the overlapping species, on the two types of lignocelluloses (>10%) were A. fumigatus (35.4%), Paecilomyces variotii (13.9%) and A. terreus(12.6%). These taxa correlated with the temperature of the collected samples. Fungal abundance was highest on SCBs from Site II (10 species), and the species diversity (1.90) and evenness (0.60) were the greatest on both lignocelluloses from Site II. The lowest diversity was observed on SFCs from Site III (1 species). A comparison of the fungal communities on the two lignocelluloses and at the three selected sites revealed few differences in species composition