Edible bamboo species are now domesticated and commercialized because of their nutraceutical values. The production of edible bamboo species are restrained by diseases caused by pathogenic bambusicolous fungi valued at 40% losses of the total $818.6 million generated annually in bamboo trade in North East India. Based on a systematic survey performed for 2 years in succession, only one Basidiomycota, a Perenniporia sp. was identified and validated by pathogenicity test. Ascomycota was the dominant and diverse group of pathogenic bambusicolous fungi. Some rDNA locus sequences failed to match sequences in the up-to-date databases and indicated novel species or genera. Divergence study based on rDNA locus showed that pathogenic bambusicolous fungi were located in the class of Ascomycetes, Sordariomycetes, Eurotiomycetes, Dothideomycetes and Basidiomycetes. The data demonstrated for the first time that Fusarium, Cochliobolus, Daldinia, Leptosphaeria, Phoma, Neodeightonia, Lasiodiplodia, Aspergillus, Trichoderma, Peyronellaea, Perenniporia, Nigrospora and Hyporales are potent pathogenic bambusicolous fungi genera restraining the production of edible bamboo Dendrocalamus hamiltonii.