The present invention relates to the development of novel mycoherbicide for controlling Parthenium hysterophorus. The present invention also discloses fungal isolates of Altemaria sp AGPH#04 use spores, as a cell-and spore-free filtrate, a crude filtrate, or a crude suspension of the culture and optionally along with other additives. The fungal strain was observed to be particularly virulent against Parthenium. The fungal strain was deposited in NCIM as private culture collection and assigned the number NCIM 13 71. The strain was also deposit in the patent collection of the IMTECH under the terms of the Budapest Treaty and has been assigned accession number MTCC 5973. The sequence homology and phylogenic analysis of strain showed 98% nucleotide similarity with other similar genus isolate. The present invention also discloses whole genome study for identification of novel probe and primer pair sequence for use in detecting isolates that exhibit bio-control activity. The present invention also discloses process
