Maintenance of genetic resources within the National Plant Germplasm System includes preserving the genetic constituency of accessions as close to the original sample as possible. Genetic changes that can arise during seed regeneration include both an overall loss of genetic diversity within heterogenous accessions and changes in the gene frequencies within accessions. Two germplasm collections are being examined with molecular methods at the Western Regional Plant Introduction Station (WRPIS) for evidence of such genetic change. In the case of pea, gross observation of seed and plant characters indicate that vigorous plant culling during a comprehensive Pea Seedbourne Mosaic Virus eradication program a decade ago resulted in the overall loss of genetic diversity in some heterogenous accessions. Isozyme data has corroborated these observations. Molecular markers are beginning to be used, both to quantify possible genetic changes in accessions as a result of the eradication process, and to document success in reintroducing diversity by repeating the eradication process with additional seed from archival seedlots. In the case of ryegrass, the practice of bulking the seed harvested from regeneration plots may bias the seedlot toward genotypes that are more fruitful. Isozyme analysis after two regeneration cycles showed that balanced sampling (equal seed no./plant) maintained allele frequencies close to the original seed sample. A bulk harvest sample and a sample with an equal number of spikes harvested from each plant showed some significant change in allele frequency, but no significant changes were seen in the allelic richness of accessions, or in the level of an accession's overall heterozygosity. A regeneration sample with an equal number of seed/plant will therefore best preserve gene frequencies within accessions, but loss of an accessions overall diversity will not diminish as a result of less than ideal sampling methods in ryegrass.