Background: Trichuriasis is an important soil-transmitted helminth infection caused by Trichuris trichiura. About one-tenth of the world population may be infected. Incidentally, T. vulpis or dog whipworm has been reported to infect humans based on the egg size. However, an overlapping egg dimension occurs between T. trichiura and T. vulpis leading to the potential for misdiagnosis. Objective: Develop a PCR method to differentiate T. trichiura and T. vulpis eggs in stool samples and to investigate the prevalence of both whipworms in humans and dogs in a rural community in Thailand. Materials and methods: We determined and compared the small subunit ribosomal RNA sequences of both species of whipworms for developing species-specific PCR diagnosis. After validation of the method, we conducted a cross-sectional survey at Ta Song Yang District in Tak Province, northwestern Thailand in 2008. Stool samples were randomly recruited from 80 schoolchildren (36 males, 44 females) and 79 dogs in this community. Results: Fifty-six individuals harbored Trichuris eggs in their stools. The PCR-based diagnosis revealed that 50 cases were infected with T. trichiura and six (10.7%) were co-infected with both T. trichiura and T. vulpis. Although the dimension of Trichuris eggs provided some diagnostic clues for species differentiation, a remarkable variation in the length of these whipworm eggs was observed among samples that could lead to misdiagnosis. Conclusion: Both T. trichiura and T. vulpis eggs were detected in stool samples of dogs that roamed around this community, highlighting the potential reservoir role of dogs in the transmission of both human and dog whipworms in this population.