An indigenous fungal culture, isolated from diseased water hyacinth, in Bolpur, Santiniketan, West Bengal, India, was found to be causing severe blight and dieback disease on water hyacinth, under laboratory and field conditions. It was subjected to morphological and molecular characterization by amplification of 18S RNA gene fragment from genomic DNA using 18S gene universal primers. Subsequently with sequencing, GenBank database comparisons and phylogenetic analysis, the fungus was determined as Alternaria japonica Yoshii. Further the pathogen was evaluated for its host specificity to be developed as mycoherbicidal agent against this invasive weed. Host range of A. japonica was screened against 48 plant species in 42 genera representing 22 families in pot experiment. Water hyacinth was the only species strongly susceptible to spore suspension (5 × 105 conidia/ml) of A. japonica. Minor infection was observed on goosefoot which is not only a weed but also ecologically separated from water hyacinth. Thus, the use of this pathogen in the biological control of water hyacinth would be safe for plants of economic and ecological significance in India. The secondary metabolite produced by A. japonica was sprayed on the test plants but phytotoxic symptoms were produced on nine out of 48 plants tested, demonstrating that phytotoxin produced by the fungus is not host specific. Further field tests needs to ascertain its efficacy under more natural conditions.