An integrated approach for genotypic and phenotypic characterization of the wheat yellow/stripe rust pathogen (Puccinia striiformis f. sp. tritici) is presented. Nineteen codominant simple sequence repeat (SSR) markers and differential sets consisting of near-isogenic lines of Avocet spring wheat, lines from previously defined “World” and “European” sets, and additional varieties showing race specificity, allow for a combined assessment of multi-locus genotype (MLG) and race. This has resulted in a unique definition of named genetic groups, many of which have had major regional or global impacts. Each genetic group may contain from one to multiple closely related MLGs and races, depending on the prevalence and the number of years since its first detection. The new approach of genotyping incoming samples may reduce redundant and time-consuming race testing of multiple isolates belonging to the same genetic group (and MLG) sampled within the same epidemiological area and year.