Macrophomina phaseolina (Tassi) Goid causes charcoal disease of oilseed plants. In this study 24 isolates, which were obtained from sunflower, soybean and sesame, were compared based on chlorate phenotypes and pathogenicity tests. For chlorate phenotypes, the isolates were grown on potassium chlorate and stored at 30oC in darkness. For pathogenicity test, seeds of sunflower, soybean and maize plants were placed on 6 – day – old colonies of each Macrophomina isolates grown on PDA and kept at 30oC in the dark. Results indicate that the sesame isolates had more colony radius rate on chlorate minimal medium in comparison to the soybean and sunflower isolates. The sesame isolates were chlorate resistant and grew normally with numerous dark microsclerotia production on the potassium chlorate. The soybean and sunflower isolates were chlorate sensitive and divided into two classes. Class 1, include the isolates that grew sparsely with a feathery like pattern, and the other one had a completely restricted radial growth meaning that M. phaseolina isolates differed in their ability to use certain nitrogenous compounds. Analysis of variance showed a significant difference between the colony radius rates of the isolates at 1% probability level. Based on Duncan’s test, the isolates have been divided in 14 classes. Results of pathogenicity test showed that there was significant difference (P< 0.01) between the isolates. The results confirmed that the feathery like pattern of the isolates was more virulent on soybean and sunflower.