Molecular markers are being used extensively for genotyping germplasm collections at the Western Regional Plant Introduction Station, Pullman WA.  Molecular markers used include isozymes, chloroplast, RAPD's, AFLP, and SSR's.  Their use has led to improvements in regeneration methods, characterization of collection diversity, identification of outliers, and detection of misidentified accessions and duplicates.  Markers have also been used to develop core collections.  Correlation of random molecular diversity with phenotypic diversity, when significant, is often weak, suggesting that both molecular and phenotypic evaluation is needed for a complete understanding of collection diversity.  Molecular markers have become an important tool to enhance evaluation and management of germplasm collections.