Natural variation in blueberry plants and conventional disease management practices may generate selective pressures on populations of Monilinia vaccinii-corymbosi, the fungal plant pathogen responsible for mummy berry disease of blueberry. In particular, the timing of development of lowbush blueberry plants may act as a selective pressure on this fungus to adapt to germinate and produce ascospores in synchrony with the bud and leaf development of blueberry clones which it infects. Fungicide use may result in more fungicide insensitive genotypes in conventionally managed lowbush blueberry fields than in fields where these fungicides are not used. We attempted to determine the genetic variation in populations of M. vaccinii-corymbosi using microsatellite markers, and the variation in fungicide resistance by determining the concentration of fungicide necessary to reduce fungal growth by 50% (EC₅₀). Forty sets of microsatellite primers developed for other species within the family same family as M. vaccinii-corymbosi were tested. Twenty-nine of the primer sets amplified DNA from M. vaccinii-corymbosi; however, none of the microsatellite primers tested appeared to amplify microsatellite loci. The fungicide sensitivity of M. vaccinii-corymbosi isolates from 3 types of fields: 4 conventionally managed, 3 organically managed and 1 unmanaged, was determined for propiconazole and fenbuconaozle, the commonly used fungicides.A baseline EC₅₀ for each fungicide was established using the fungicide sensitivity data of isolates from the unmanaged area. The baseline EC₅₀ was significantly higher for propiconazole (0.016 µg/mL) than fenbuconazole (0.00059 µg/mL). No significant differences in the fenbuconazole EC₅₀ were found among management types. The propiconazole EC₅₀ for conventionally managed fields (0.020 µg/mL) was significantly higher than for the unmanaged area (0.016 µg/mL).  The propiconazole EC₅₀ for organically managed fields (0.018 µg/mL) was not significantly different from those of the other field types. The continual, biennial use of the fungicide propiconazole on populations of M. vaccinii-corymbosi may cause the development of fungicide insensitivity over time. Lowbush blueberry growers should carefully monitor their fields for fungicide resistance, and consider using non-DMI fungicides, alternations of fungicides or fungicide mixtures to protect against mummy berry blight.