Abstract Commercial production of pecans in the southeastern U.S. relies on fungicide applications to control scab, caused by Fusicladium effusum. Under intense disease pressure, 10–15 applications may be made per season and the potential development of fungicide resistance is a major concern. A rapid method was developed to determine sensitivity of the pathogen to protectant chemicals based on conidia germination, and to fungicides active on post-appressorial pathogen stages based on micro-colony growth. This method uses conidia transferred directly from lesions to fungicide-amended media. Using this method, sensitivity profiles were determined for isolates from three non-treated orchards with little or no fungicide use histories and from 33 commercial orchards in 2008 with a history of fungicide use. Compared to the non-treated orchards, significant reductions in in vitro sensitivity were detected in 20 orchards to fentin hydroxide, in 4 orchards to dodine, in 6 orchards to thiophanate-methyl and in 20 orchards to propiconazole. The novel methodology will be useful for monitoring fungicide sensitivity of F. effusum populations and evaluating resistance management programs in commercial pecan orchards.