The present publication reports the mycobiota associated with Eichhornia crassipes (C Mart.) Solms (Pontederiaceae) infesting the Harike Wetland at Punjab in India and their potential application as a biological control agent based on their pathogenicity to the host plant. Of the 30 fungal isolates recovered from the infested samples of E. crassipes only one isolate #19BJSS caused 98% damage or infestation to the leaves during the in vitro leaf bioassay while it exhibited 100% plant death during the whole plant bioassay after 168 hours post inoculation (hpi). Morphological studies revealed it to be a member of Botryosphaeriaceae family which was further confirmed by Internal Transcribed Spacers (ITS) phylogenetic studies wherein the isolate #19BJSS clustered with Diplodia mutila. Botryosphaeria species have been predominantly associated with canker and die back diseases of woody plants. This is the first report of occurrence of Diplodia mutila #19BJSS as a pathogen of E. crassipes and for its potential as a biological control agent for the management of water hyacinth.