Pathogenicity of fourteen isolates of Fusarium moniliforme, from different cotton-growing areas of Egypt was evaluated on cotton cultivar Giza 86 under greenhouse conditions. All the tested isolates were pathogenic. They affected all disease variables. Isolates no_s. 3, 13, 1, and 10 were the most pathogenic isolates in pre-emergence stage, while isolates no_s. 2, 10, and 3 were the most pathogenic isolates in post-emergence stage. All isolates were more pathogenic in pre-emergence stage than post-emergence stage except isolate no. 2, which was more pathogenic in post-emergence stage. All tested isolates  significantly reduced both of  plant height and dry weight of seedlings. There were no relationship between pathogenicity of the isolates and their geographic origins. There was a negative significant correlation between pre-emergence damping-off and the dry weight of seedlings. Also, there was a negative significant correlation between post-emergence damping-off and survival. Cluster analysis of isolates based on pathogenicity patternes showed that there was no relationship between virulence patternes of isolates and their geographic origin. Electrophoretic protein profiles of isolates showed that the population of Upper Egypt was genetically differed from that of Nile Delta. There was a correlation between protein profiles and geographic origin of isolates, while there was no correlation between protein profiles and pathogenicity of isolates.