A rapid and cost efficient technique was developed and used to generate 168 sequence tagged microsatellites (STMs) in the barley scald pathogen Rhynchosporium secalis. Sixty-two STMs, amplifying 66 loci, revealed a high level of polymorphism among a diverse set of 16 Australian isolates. Each locus revealed two to nine alleles (average 4 ± 1.82), and a gene diversity measure of 0.54 was obtained. This technique not only halved the cost of marker development compared to traditional methods, but substantially reduced the cost of performing fluorescence-based microsatellite assays. These STMs provide a powerful tool for genetic studies in R. secalis.