The loach is widely distributed in China and cultivated enormously with the price increased in recent years. Its sex determination type and sex chromosome has not been recognized. In the present study, we report a novel sex-specific DNA marker in loach Misgurnus anguillicaudatus. The animals used in our experiments were collected from a wild population in wetland on the ancient Yellow river, Yanjin Country, Henan Province. 220 random primers were used for random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) with the genomic DNA from two sex individuals as template. When using the S2111 primer, a novel 1040 bp sex-specific PCR product was amplified from known male fish. This fragment of DNA was cloned and sequenced. Two primers (MAmf1-P1 and -P2) were designed from the cloned sex-specific sequence to amplify the male-specific fragment using PCR for sexing, with the house-keeping gene beta-actin as positive control. Sex-specific bands in the gel were represented in the males but none were found in the females. The PCR products in the gel were then transferred onto nylon membranes and hybridized with a DIG-labeled probe of the cloned male-specific DNA fragment. Clear hybridization signals were found only in the male loach. The same result was obtained from dot blotting hybridization. The fragment is a repetitive DNA, and presents its closely related species Paramisgurnus dabryanus but not linked to sex. The cloning of the male-specific DNA laid a good foundation for the isolation of gender-specific chromosome segments with chromosomal walking or gene library, and improved the mechanism exploration of sex chromosome evolution in fish.