Trichuris suis is a common parasite in pigs that is thought to infect humans based on studies using recently developed molecular methods. However, the utility of such molecular methods for detection has not been examined. In the present study, we assessed PCR- and sequencing-based molecular methods for the detection of several stages of T. suis. PCR targeting the mitochondrial large ribosomal subunit was successful with amplification of DNA from the samples. The sequences of the isolates formed a phylogenetic cluster with isolates from China and Ecuador. The assay was effective by using DNAs extracted from a low number of eggs (> 20 eggs) and the fragments of worms after histopathologic analyses. This is the first report describing the molecular identification of T. suis from pigs in Japan.