This research aims to study the isolates of pathogenic fungi under a microscope with their visualization using fluorescent staining. Phytopathogenic fungi Fusarium sp. were assessed using real-time PCR. The highest concentration from the standard F. cerealis series (3,000, 300, 30, and 0 ng DNA/mL) showed a Ct value of 26, while the non-matrix control Ct was almost 40 for both fungus and plant primers. Amplification curves were also obtained for healthy and infected barley stems and leaves. DNA extracts from the infected barley stems and leaves showed a Ct value ranging from 26 to 30. These results corresponded to the concentrations of 300-3,000 ng/mL of F. cerealis and F. proliferatum DNA, respectively. At Ct 36, the DNA content in healthy barley leaves and stems was the same as in non-matrix controls. The dissociation curves for F. cerealis DNA extracted from the infected barley stems and leaves peaked at 87ºC, thus being identical to the peak obtained with pure F. cerealis DNA. To prevent the infection of barley crops with phytopathogenic fungi, it is necessary to apply an integrated approach, which involves ecological principles of protection. Following this strategy, it was possible to successfully apply crop rotation and tillage.