This study analyzes the performance of a method to isolate microsatellites from largely unknown target genomes. This reporter genome protocol (RGP) utilizes naturally occurring repeat motifs in genomes of distantly related organisms as hybridization probes. The RGP proved very successful in all 13 enrichment reactions from eight marine target species (comprising a dinoflagellate, a diatom, and six arthropod species), yielding on average 85.5% positive colonies. The RGP naturally screens for all repeat types occurring in the reporter genomes and is therefore less biased than standard protocols that typically test few, short motifs only. Using the genomes of Mus musculus, Drosophila melanogaster, and Homo sapiens as reporter genomes in this study, 133 different di- to hexanucleotide repeat types were obtained. Success of the RGP did not depend on overall microsatellite density in the reporter genome but increased with genetic distance between target and reporter genomes because hybridization to conserved nonrepeat regions is less frequent. Relative abundance of repeat types in the reporter genome had a significant effect on repeat type frequencies in the target library. Altogether, the RGP greatly simplifies the isolation of microsatellites from unknown genomes and makes microsatellite markers more attractive for a wide range of studies.