Seventy one fungal isolates were isolated from cotton plants in Kafrelshiekh. These isolates were identified as Rhizoctonia solani, Fusarium sp., Macrophomina phaseolina and Scloratium rolfsii. Rhizoctonia solani was the most frequent fungus among the isolated fungi where it recorded 39.43% followed by Fusarium sp. 29.57%, Macrophomina phaseolina (23.49%) while Sclerotium rolfsii was the least frequent fungus (7.04%). Under artificial inoculation, cv. Giza 86 was the most highest infective one among the other tested cotton Cvs where was recorded with it. Percent of pre- and post- emergence. As for controlling cotton root rot disease. Some bioagent like (Bacillus Subtilis) and (Trichoderma harzianum), Bio- Zeid, Bio-arc and Plant guard as commercial formula, in addition to antioxidants like salicylic acid, acetic acid and citric acid and microelements like iron chelate, zinc chelate and manganese chelate were tested. Against the causal pathogen of cotton root rot under greenhouse conditions. Under field, all treatments except citric acid and plant distance at 40cm led to significant increase in percentage of survived plants. In this respect, B. subtilis, T. harzianum, Plant guard, Bio- arc, Salsylic acid, Rizolex-T and Moncut recorded efficiency more than 71.24% compared to check treatment. Most of the treatments did not show a significant increase in the disease severity except B. subtilis, T. harzianum, Plant guard, Bio- arc and Salsylic acid, which led to reduction significant in disease severity comparing to the control treatment. On the other hand, non-significant differences in boll weight as a result of using the various treatments, meanwhile there were significant different in the number of fruiting branches/plant. The highest number of fruiting branches were recorded with Bio-zeid and plant distance at 45 cm, respectively during season 2014 and 2015. Also, there were clear significant differences between treatments for earliness index during two seasons. Whereas non-significant differences were recorded with seed index or lint% among the different tested treatments.