Objective To screen microsatellite DNA markers from genome of guinea pigs for further genetic quality control and gene-mapping of this species .Methods Microsatellite sequences were obtained by magnetic bead enrichment and genome database screening , and candidate loci were chosen to design primers .Thereafter , genomic DNA of 5 different guinea pig strains were employed to select polymorphic microsatellite DNA markers based on PCR amplification results .Re-sults A total of 304 microsatellite sequences were analyzed by magnetic bead enrichment and 125 primers were designed . One polymorphic microsatellite DNA marker and 17 specific sites ( no polymorphic was found ) were determined .By gene-mapping , 292 microsatellite sequences were obtained and 178 primers were analyzed , totally 25 polymorphic microsatellite DNA markers and 28 specific sites ( without polymorphics ) were discovered .Conclusions We obtained 26 polymorphic microsatellite DNA markers and 45 potential markers in guinea pigs , and these may lay a foundation for application of mic-rosatellite DNA markers in genetic quality control and gene-mapping of guinea pigs .