Our attempts to find RAPID markers linked with resistance genes to Septoria and Tilletia relying on co-segregation and to test the SSR markers, identified in literature, in order to select bread wheat resistant to Septoria and Tilletia are presented. Several candidate RAPD markers possibly linked with Septoria resistance genes and fewer linked with Tilletia resistance genes were identified. Some RAPID and SSR markers were specific for some resistant lines. These markers,. probably, marked different resistance genes in different lines. It seems that some Septoria resistance genes came from rye genome because these genes were marked with some primers specific for rye genome. We found segregation for these markers in several lines, indicating that the analyzed lines were not completely stabilized. The ISSR markers used could not discriminate the resistant from susceptible genotypes to Septoria and Tilletia.