Cluster analysis was used to evaluate the genetic diversity among 12 cotton genotypes highly resistant to Fusarium wilt disease. Cluster analysis was carried out based on electrophoretic banding patterns of peroxidase isozymes and seed proteins. Cluster analysis of peroxidase isozymes divided the genotypes into three distinct remotely related groups. Peroxidase isozymes were reliable to differentiate among genotypes included in the different groups; however, the isozymes were of limited reliability to differentiate among genotypes within groups. The genotypes were separated into a larg number of remotely related subclusters based on cluster analysis of their protein banding patterns. Therefore, it was easy to differentiate among the genotypes of the different subclusters. The present study demonstrated that cotton genotypes could be identified by their electrophoretic banding patterns of peroxidase isozymes and seed proteins. These results could be of practical value for cultivar identification and for seed purity tests.