12Fusarium species are distributed widely in ecosystems of a wide pH range and play 13 a pivotal role in the aquatic community through the degradation of xenobiotic 14 compounds and secretion of secondary metabolites. The elucidation of their genome 15 would therefore be highly impactful with regard to the control of environmental 16 pollution. Therefore, in this study, two indigenous strains of aquatic Fusarium, QHM 17 and BWC1, were isolated from a coal mine pit and a subterranean river respectively, 18 cultured under acidic conditions, and sequenced. Phylogenetic analysis of these two 19isolates was conducted based on the sequences of internal transcript (ITS1 and ITS4) 20 and encoding β-microtubulin (TUB2), translation elongation factors (TEFs) and the 21 2 second large sub-unit of RNA polymerase (RPB2). Fusarium, QHM could potentially 22 represent a new species within the Fusarium fujikuroi species complex. Fusarium 23 BWC1 were found to form a clade with Fusarium subglutinans NRRL 22016, and 24 predicted to be Fusarium subglutinans. Shot-gun sequencing on the Illumina 25Hiseq×10 Platform was used to elucidate the draft genomes of the two species. Gene 26 annotation and functional analyses revealed that they had bio-degradation pathways 27 for aromatic compounds; further, their main pathogenic mechanism was found to be 28 the efflux pump. To date, the genomes of only a limited number of acidic species from 29the Fusarium fujikuroi species complex, especially from the aquatic species, have 30 been sequenced. Therefore, the present findings are novel and have important 31 potential for the future in terms of environmental control. 32 33 IMPORTANCE Fusarium genus has over 300 species and were distributed in a 34 variety of ecosystem. Increasing attention has been drawn to Fusarium due to the 35 importance in aquatic community, pathogenicity and environmental protection. The 36 genomes of the strains in this work isolated in acidic condition, were sequenced. The 37 analysis has indicated that the isolates were able to biodegrade xenobiotics, which 38 makes it potentially function as environmental bio-agent for aromatic pollution 39 control and remediation. Meanwhile, the virulence and pathogenicity were also 40 predicted for reference of infection control. The genome information may lay 41 foundation for the fungal identification, disease prevention resulting from these 42 3 isolates and other "-omics" research. The isolates were phylogenetically classified 43into Fusarium fujikuroi species complex by means of concatenated gene analysis, 44serving as new addition to the big complex. 45 46 47 48