We cloned duck microsatellite repeat sequences from genomic DNA of an Indonesian native duck to evaluate the genetic relationships among native breeds of duck. A (CA)_n-enriched library was constructed using the method of Takahashi et al. (1996) with modifications. In the library, 8.3% of the clones were CA-positive. The average number of uninterrupted (CA)_n repeats among 22 duck microsatellites was 11.4. Fifteen clones which could be developed as PCR primer pairs to detect (CA)_n repeat length polymorphisms were identified. They should provide a valuable tool for studies related to biodiversity and population structure in duck.