Cladosporium spp. is a potential mycoparasite for controlling some rust fungi. The aim of the research was to obtain the effectiveness of 10 Cladosporium spp. isolates was found in chrysanthemum central area (Cianjur and West Bandung District) and genetic relationship among the isolats. The research carried on April to Agustus 2014 in Micology Laboratory Indonesian Ornamental Crop Institute and Pathology and Silviculture Laboratory, Faculty of Forestry, Bogor Agricultural University. Pathogenicity of the 10 fungus isolate was tested against rust pustules on chrysanthemum leaves and genetic relationship between isolates was analyzed by electrophoresis isozyme using EST, ACP, and PER enzyme. The results showed that nine of Cladosporoium spp. isolates were effective parasited rust pustule with more than 50% effectiveness. The cluster analysis based on isozyme analysis showed that Cladosporium spp. isolate have two distinc groups with 67% similarity coefficient.