The present investigation was performed during the season June 2013 to June 2014. In this investigation direct method of study were used, includes isolation and direct observations. During these investigation 16 dominant fungi was isolated. Comparative analysis was done as organic cotton field fungi and conventional cotton fungi field. Fungal pathogen of organic field is higher than that conventional cotton field. Total fungal population was higher in organic cotton fields with the age of cotton plant as compare to conventional cotton fields; While Pathogenic fungal population was higher in conventional cotton field as compare to organic one. Alternaria alternata, Alternaria macrospora., Aspergillus flavus, Aspergillus niger, Cercospora gossypina, Colletotrichum gossypii, Curvularia lunata, Drechslera tetramera, Helminthosporium gossypii, Penicillium notatum, Penicillium chrysogenum, Rhizoctonia solani, Stemphylium solani, Rhizopus oryzae,Trichoderma harzianum, Trichoderma viride were reported. It was reported that Alternaria, Penicillium and Aspergillus were the most common fungi observed in both the farming systems.