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The recent taxonomic diversification of bacterial genera <i>Pectobacterium</i> and <i>Dickeya</i>, which cause soft rot in plants, focuses attention on the need for improvement of existing methods for the detection and differentiation of these phytopathogens. This research presents a whole genome-based approach to the selection of marker sequences unique to particular species of <i>Pectobacterium</i>. The quantitative real-time PCR assay developed is selective in the context of all tested <i>Pectobacterium atrosepticum</i> strains and is able to detect fewer than 10² copies of target DNA per reaction. The presence of plant DNA extract did not affect the sensitivity of the assay.