We amplified D1 and D3 expansion segments of the 28S ribosomal RNA from 10 Suanguina moxae populations found in Korea. The amplification of the D1-D3 expansion segments of 28S gene of all populations tested produced a single PCR product approximately 1.03kb in size, suggesting the lack of D1-D3 expansion region size polymorphism among populations. The secondary structure model of 28S expansion segments D2 and D3 for Subanguina Moxae was predicted based on free energy minimization with comparative sequence analysis and new sequence alignment was conducted based on predicted secondary structure model. The predicted model was compared with previous predicted models of plant and animal parasite nematode. This predicted secondary structure model will provide valuable information to allocate positional sequence homology and reconstruction of reliable phylogenetic trees.