The Scandinavian eagle owl population decreased to a few hundred individuals during the first 80 years of the last century as a result of hunting, collecting of chicks, and reproductive problems because of pollution. When most threats against the population were gone, supportive breeding was initiated. Since then the population has recovered remarkably. We describe how seven polymorphic microsatellite markers (Bb-42, 100, 101, 111, 126, 131 and 145) were developed from an enriched genomic library. These loci have three to 12 alleles and observed heterozygosities ranging from 0.20 to 0.94 in a sample of 66 individuals from a Swedish captive population.