The partial NADH dehydrogenase subunit 4 (pnad4) fragment was amplified by polymerase chain reaction (PCR) from Schistosoma japonicum collected from 4 areas in Hunan province, and the amplicons were cloned and sequenced. A 480 bp sequence was obtained and the nucleotide difference between samples from the four locations were 0.4%-1.3%. Low level of sequence variability between and within different populations of S. japonicum was detected. The results are worthwhile for further study on the population genetic structures of S. japonicum.