A method is described for the routine diagnosis of Spongospora subterranea on potato tubers. Accurate diagnosis of powdery scab can be difficult and usually relies on observation of resting spores (cystosori) within the scab lesions on diseased tubers. A fast automated extraction method was combined with a real-time PCR assay using TaqMan® chemistry to improve and advance routine diagnosis of powdery scab on tubers. The diagnostic assay was made more reliable by using as an internal control potato DNA (cytochrome oxidase) which took into account differences in extraction efficiency and guarded against false negative results. The diagnostic assay was validated by testing 37 scabbed tuber samples of various cultivars collected from fields in different locations in the UK. The assay successfully detected S. subterranea in all samples with suspected powdery scab; it also detected S. subterranea in tubers in which cystosori were present and in tubers in which cystosori were not observed. The TaqMan assay was found to be at least 100 times more sensitive than conventional PCR and ELISA.