The fungal disease, Charcoal rot, caused by Macrophomina phaseolina is becoming one of important pathogen in sunflower production, mostly expressed in areas with high temperatures and dry conditions. Development of tolerant sunflower genotypes is the most reliable way to control this disease. It is important to find proper evaluation method which can provide accurate insight in potential genetic control of tolerance in sunflower. The aim of this work is: to compare two inoculation methods of sunflower with M. phaseolina, to compare the tolerance of inbred lines to this pathogen and to determine which method gives better insight into the inheritance of tolerance in sunflower. The experiment was determined under greenhouse conditions and two methods were used. The Unwounded stem base infection method (USBI), is less aggressive approach where the infection is similar to natural conditions. While for the toothpick method (TM) inoculation it is necessary to puncturing the tissue with the toothpick and create the entrance for pathogen infection. Four inbred lines were used in research which was created at the Institute of Field and Vegetable Crops, Novi Sad (IFVCNS)