Apart from the diseases, several weed fungi are found to grow over the bed. For example, the white plaster mould Scopulariopsis fimicola and a very similar fungus Verticillium agaricicotum are common moulds of paddy straw mushroom. In case of cotton waste compost using substrate, Thielavia terricola, Trichoderma sp, Aspergillus sp, Pythium sp, and Rhizoctonia sp, are the common occurrence in paddy straw mushroom cultivation. In India, the mould, like Chaetomium sp, Alternaria sp, and sordaria sp, are observed when wheat, barley, jowar, etc. are used as substrates. In case of paddy straw substrate, several Coprinus species, like C. aratus, C.cenerreus, C.Lagopus, etc. and various other mould, such as Psathyrella sp, Penicillium sp, Podospora favrelli, Aspergillus sp, Rhizoctonia solani, Rhizopus sp, and Sclerotium sp, are the common weeds in paddy straw mushroom cultivation in India. The damage caused by Coprinus sp,is the greatest problem in paddy straw mushrooms. The mould completes its life cycle in shorter duration (1 week) than the straw mushrooms.
The best measure to obtain good yield with minium growth of Coprinus is by keeping C:N ratio of substrate in the range of 40:1 to 50:1. The moisture content of the substrate should be kept in range of 60 to 65 percent, since the high moisture favours the growth of Coprinus. Several additional method are being used to control the diseases and moulds.
The pasteurization is one of the motst effective measures to control them. Partial disinfection of the straw by dipping the straw bundles in carbendazim (75 ppm) and formalin (500 ppm) mixed solution for 10 minutes before bed preparation is also used to minimized the diseases and moulds. Partial sterilization of straw and spraying of zineb (0.2 %) or captan (0.2 %) are also suggested to manage the diseases and mould in paddy mushroom cultivation.