This work addresses the application of a new group of molecular markers, microsatellite loci, to monitor genetic diversity in stocks used in fish enhancement programs. To illustrate the potential use of these markers, we examined the genetic variation associated with the Connecticut River and Penobscot River populations of Atlantic salmon Salmo salar in the United States. Both rivers are stocked annually with fry from captive or cultured stocks that are one generation removed from sea-run adults. We analyzed microsatellite loci variation among sea-run adults and the derived cultured stock for the Connecticut River in a given year, along with two consecutive cohorts of cultured age-0 juveniles for the Penobscot River. Our results reveal subtle differences in allele frequencies between the two samples for each stock and some potential increases of homozygotes. These results demonstrate the potential value of microsatellite loci for routine genetic monitoring of cultured Atlantic salmon populations associated with restoration programs in the eastern United States.