A rapid and relatively cost-effective method was developed to isolate and purify RNA from mycelia of two plant-pathogenic fungal species of the genus Fusarium, F. graminearum and F. coffeatum, with different morphological and biochemical properties. The method utilizes a guanidine hydrochloride-based buffer and spin columns from a commercial plasmid DNA extraction kit and can be applied to both mycelia grown on nutrient agar media and liquid fungal cultures. The RNA yield with the method was 4-14 μg/100 mg of mycelium dry weight, and the RNA integrity number (RIN) values were up to 8.4. Method optimization showed that preliminary freeze drying is advisable to perform in the case of liquid cultures and that an RNase inhibitor should be used in the case of late culture growth stages.