The present invention deals with a mycoherbicidal isolate of Setosphaeria monoceras sp. or extracts obtained therefrom, useful for the control of Water hyacinth. The present invention also discloses biological control compositions comprising fungal isolate extract formulated in a growth medium for maintaining the viability of extract when the biological control composition is applied to weed. The present invention also discloses methods of screening fungal isolate to determine if they exhibit biocontrol activity. The present invention also discloses use of Setosphaeria monoceras strain. In yet a further aspect the invention relates to use of an Setosphaeria strain for producing a herbicidal agent effective for controlling growth of water hyacinth plants. The strain used preferably is a strain having the characterizing features of Setosphaeria strain AGWH#1 1 as deposited at IMTECH under accession number MTCC 5974. The present invention to provide the 18s rRNA sequence analysis showed 96% nucleotide similarity of the Fungi to Setosphaeria monoceras. (AGBIO designated AGWH#1 1/NCIM1370/MTCC 5974) but also indicated nucleotide variation of this fungus from other known genus of Bipolaris, Pleosporaceae, Cochiliobolus, Alternaria including an environmentally acceptable alternative to synthetic chemical herbicides for the control of weeds, such as Water hyacinth. The present invention also discloses methods of whole genome study of strain.