Microsatellites are molecular markers with high resolving power and therefore a valuable tool for studying microevolutionary processes. However, identification of microsatellites and initial setup can be a labour intensive and time consuming task. We are applying microsatellites in a study aiming to understand the evolution of the Antarctic benthos and the mechanisms leading to the surprising high diversity in the Southern Ocean.We employed a novel cross-genome hybridization technique for the Antarctic giant isopod species complex Ceratoserolis trilobitoides which does without radioactivity and time consuming screening procedures. A main advantage is that no assumptions have to be made concerning the type of repeats to be screened for. Compared to two radioactive screening methods and another PCR-based, non-radioactive isolation technique (PIMA), the enrichment was very effective with 70-95% of the screened colonies containing short sequence repeats. As much as 50 different microsatellite types were detected within the 140 inserts screened.