A part of the mitochondrial cytochrome c oxidase subunit I (COI) gene and the nuclear ribosomal DNA second internal transcribed spacer 2 (ITS2) of a newly described lung fluke, Paragonimus pseudoheterotremus, were sequenced and compared with P. heterotremus, the species with a similar morphology. Pairwise distance of COI sequences revealed a genetic difference between P. heterotremus and P pseudoheterotremus with a nucleotide difference of COI sequences between these two species of 10.6%. The constructed phylogenic tree with high bootstrap proportion suggested that P. pseudoheterotremus is a sister species of P. heterotremus.