Abstract: In this study, an in silico approach was utilized to identify homologies existing between common carp microsatellite sequences and GenBank database using Blastn and Blastx searches. About 875 microsatellite sites with flanking sequences over 50 bp of common carp were first compared to the zebrafish EST database. The results showed that 121 homologies were found using Blastn. Subsequent Blastx searches confirmed 94 sites recorded in the protein database. Except for 33 hypothetical proteins and three unknown proteins, seven out of 58 characterized proteins have been mapped to two linkage maps. In addition, two polymorphic STS markers were developed using matched zebrafish EST sequences by PCR-SSCP method, of which one marker HLJZe33 was mapped successfully. This study was a pilot for comparative studies between common carp and zebrafish, and the results demonstrated that more genetic and genomic resources of zebrafish can be used for the genome research of common carp.