The purpose of this study was to analyze sequence variation in the partial mitochondrial ribosomal large subunit gene (prrnL) among Trichuris ovis (T. ovis) isolates from Guangdong province, China and to study the phylogenetic relationships of T. ovis with other whipworms using prrnL sequences. The prrnL sequences were amplified from individual T. ovis samples by polymerase chain reaction (PCR) method and the obtained prrnL sequences were aligned using ClustalX 1.81. Maximum parsimony (MP) tree was constructed using the software PAUP 4.0 Beta 10. The lengths of all prrnL were 849850 bp, and differences in prrnL sequences within T. ovis were 00.8%. Phylogenetic analyses showed that all T. ovis isolates were clustered in the same clade. The prrnL sequences were quite conserved within whipworm species while inter-species differences (33.4%36.1%) were obvious. Thus prrnL sequences can be used as a useful marker for the differentiation and identification of different whipworms.