Stripe rust of wheat, caused by Puccinia striiformis f. sp. tritici, is one of the most destructive diseases in the region west of the Rocky Mountains and has become increasingly important in the region east of the Rocky Mountains in the United States. Stripe rust of barley, caused by P. striiformis f. sp. hordei, has established in the south central states and the Pacific West since its first detection in Texas in 1991. The rusts have been monitored throughout the Pacific Northwest and through collaborators throughout the country. Stripe rust samples were tested on a set of 20 wheat genotypes used to differentiate races of P. striiformis f. sp. tritici or a set of 12 barley differential genotypes to differentiate races of P. striiformis f. sp. hordei. From 2000 to 2004, 56 new races of P. striiformis f. sp. tritici and 20 new races of P. striiformis f. sp. hordei were identified. Frequencies and distributions of races were annually determined. To screen germplasms and evaluate breeding lines for stripe rust resistance, thousands of wheat and barley entries were tested in several field locations under natural infections and in greenhouses with selected races of the pathogens. Genetics of resistance in important genotypes of wheat and barley were determined and molecular markers were developed for a numerous resistance genes. A bacterial artificial chromosomal (BAC) library of a hexaploid wheat line was constructed to clone resistance genes. A BAC and full-length cDNA libraries were constructed to determine the P. striiformis genome and study the functional genomics of the pathogen. Fungicides were tested for their efficacies in stripe rust control. Yield reduction by stripe rust and yield increase by fungicide application of wheat and barley cultivars were determined to ensure appropriate use of fungicides.