Fungicides have greatly contributed to sustaining quality food production through protecting a variety of crops from fungal diseases. However, such production is often threatened by the occurrence of pathogen strains resistant to fungicides. In this paper, the resistance to QoI and MBI-D fungicides in the pathogens of horticultural crops and rice blast fungus, respectively, are introduced as representative cases of resistance which have been experienced recently. Implications for integrated disease control that reduces the risk of fungicide resistance are discussed, then strategies to cope with resistance are overviewed. Application of PCR-based molecular techniques has become a powerful tool in the diagnosis of pathogens and/or fungicide resistance. Rapid and quantitative detection of resistant strains in fungal populations will make it easier to precisely predict the resistance risk without control failure by fungicides. The approach will also match the direction demanded by the society to reduce pesticide inputs to the agricultural environment.