Fungal brown spot caused by Bipolaris oryzae, and spot blotch caused by B. sorokiniana, are commonly found in cultivated wild rice paddies. Strobilurin-based fungicides are effective in reducing these diseases in the upper plant canopy. After three years of fungicide applications Bipolaris spp. populations decreased to low levels in wild rice plants early in the season, although the populations increased later in the year. Phenotypic identification of diseases based on small lesions early in the season is difficult and often misleading. To aid in an accurate and rapid detection of Bipolaris spp. pathogens, we developed SYBR Green-based PCR assays with primers designed from ITS1 and the B-tubulin genes. The assays discriminate both Bipolaris spp., and other fungal species. To maintain control of foliar diseases during the wild rice growing season, azoxystrobin-based fungicides are needed. Even though fungicide resistance is unlikely to develop in B. oryzae due to an intron after the G143 codon of the cytochrome b gene, changes toward reduced sensitivity could still occur in codons 129 and 137. To monitor changes in fungicide sensitivity, we developed a PCR assay based on TaqMan technology to detect changes from phenylalanine to leucine in position 129, while nucleotide changes in positions G143 and G137 will be monitored with SYBR Green-based assays. These assays will aid in understanding the epidemiology of wild rice pathogens and timely application of fungicides.