The objective of this study was to determine whether genetically distinct groups of Puccinia triticina are present in four regions of the Russian Federation. Collections of P. triticina were obtained from the Central, North Caucasus, Volga and West Siberia regions from 2006 to 2010. Ninety‐nine single uredinial isolates were tested for virulence phenotype with 20 Thatcher near‐isogenic lines of wheat. Forty‐one virulence phenotypes were found in the four regions, with eight in common between the widely separated Central and West Siberia regions. A total of 72 isolates were tested for molecular genotype with 23 simple sequence repeat (SSR) primer pairs, and 66 isolates were used for further analysis after clone correction for virulence and molecular genotype. Analysis of variation showed no overall differentiation of SSR genotypes or virulence phenotypes based on region of origin. Linkage disequilibria for SSR genotypes were high across the entire population. The regional populations had higher than expected levels of allelic heterozygosity that indicated clonal reproduction. Based on cluster analysis of SSR genotypes there were two groups of P. triticina isolates that were widely distributed across Russia. The two SSR groups also differed significantly for virulence. Puccinia triticina may be dispersed from a common source of inoculum in the European or Caucasus regions of Russia. The Russian P. triticina populations were highly differentiated for SSR genotype from populations in Tajikistan, Kyrgyzstan, Uzbekistan, Armenia, Georgia and Azerbaijan and more similar to populations from southern Kazakhstan and northern Kazakhstan.