Aquatic ecosystems throughout the world are threatened by the presence of invasive aquatic plants, both floating and submerged. Some of the aquatic species, such as water hyacinth (Eichhornia crassipes [Mart.] Solms), alligator weed, Alternanthera philoxeroides (Mart.), giant salvinia, Salvinia molesta D.S. Mitchell and water lettuce (Pistia stratiotes L.), Griseb. despite being relatively minor problems in their native range, have become major invaders of aquatic habitats in other parts of the world after having escaped from their natural enemies. Unchecked growth of aquatic vegetation is generally undesirable and reduces the value of the water resource. Despite adopting all control options including manual, mechanical, chemical and classical biological, the problem persists. The current weed management is oriented towards finding approaches that are effective in controlling the weed and reducing environmental contamination from herbicides. Plant pathogens have been gaining increasing attention and interest among those concerned with developing environmentally friendly, effective and compatible approaches for integrated management of the noxious weeds. This paper discusses some of the major microbial agents associated with aquatic weeds and their increasing role in integrated weed management.