Abstract: Gene mutation is the fundamental reason why many plant phytopathogenic fungi show the resistance to lots of systemic fungicides. It is important to detect relative gene mutation to reveal molecular mechanism of fungicide resistance and earlier diagnosis. Six molecular techniques have been successfully employed to detect resistant isolates of target fungus, such as Allele-SpecificAmplification(ASA), Restriction Fragment Length Polymorphism(PCR-RFLP), Allele-Specific Oligonucleotide Hybridization(ASOH), Single-Strand Conformation Polymorphism(SSCP), Quantitative Real-time PCR, Denaturing High-Performance Liquid Chromatography (DHPLC). These modern techniques can detect earlier fungicide resistance or development of resistant sub-population in field timely, quickly and accurately. The increasing use of diagnostic tools to detect fungicide resistance plays an important part in improving the rational use of fungicides for sustainable disease management systems.