Expressed sequence tags (ESTs) are of high value in genome mapping and marker-assisted selection (MAS). This study aims to develop EST markers for genome mapping and other studies of common carp (Cyprinus carpio L). A total of 7381 ST sequences (400-3500bp) were downloaded from the EST database of tire GenBank as the source data of the present analyses. Sixty-seven pairs of primers (designated as HB1-67) were designed in the 3' untranslated region (UTR) of the common carp ESTs,47 of which can successfully amplify specific products from genomic DNA. Twelve polymorphic EST markers were identified in a backcross mapping family of common carp by single-strand conformation polymorphism (SSCP) analysis. Six of the 12 polymorphic EST markers were derived from common carp genes of known function, and the rest were from common carp ESTs homologous to putative genes in zebrafish (Danio rerio) or channel catfish (Ictalurus punctatus). Allele distribution of these polymorphic EST markers was found to follow the Mendelian segregation (1:1 or 3:1) in both the backcross family and gynogenetic haploids, and the number of SSCP bands in haploid population was half of that in diploid family. The gene diversity (H = 0.437) of Dongting Lake population of common carp revealed by 4 polymorphic EST markers is much lower than that by previous microsatellite analysis (close to 1). The results of present study indicated that EST-SSCP markers, with codominant inheritance, can be used as a powerful tool in the genetics of not only diploid but also haploid common carp. As Type I marker derived from coding region with relatively lower genetic variability, EST-SSCP markers are still of high potentials in such studies as genome mapping (including genetic linkage maps and gene maps, as well as comparative mapping), genetic structure, and genetic adaptability of fish populations.