In this study, we identified a sex-specific DNA marker using randomly amplified polymorphic DNA (RAPD) fingerprinting in Yellow River carps (Cyprinus carpio from the Yellow River). Two hundred and twenty random primers were used in pooled DNA samples and individual DNA samples from male and female fish for RAPD fingerprinting. When using the primer S2107, a novel sex-specific PCR product was identified in all male individuals. DNA sequencing revealed that this 909 bp long DNA fragment has a low similarity to a repetitive sequence in zebrafish Danio rerio. In order to confirm the amplification results, two primers were designed within the male-specific sequence in order to amplify the sex-specific fragment from genomic DNA of male and female carps for sexing by PCR. The results indicated bands specific for males but not females. Respective results were obtained in dot blot and Southern blot hybridization experiments when using this sex-specific fragment as the probe. The sex-specific pattern was observed in 30 individuals from three separate common carp stocks, suggesting that the sequence is conserved in common carp species. However, no hybridization signals were found in grass carps Ctenopharyngodon idella, which are related to common carps. We submit to use this sex-specific fragment as a marker to rapidly and accurately identify the gender of Yellow River C. carpio. Furthermore, the sex-specific chromosome region may be characterized and used to study mechanisms of chromosome evolution in this fish species.