The Duffy binding domain gene structures of Plasmodium vivax facilitate the invasion of erythrocytes. Human erythrocytes that lack Duffy blood group antigens are resistant to invasion by P. vivax. We have sequenced the Duffy binding domain gene from eight P. vivax isolates collected from malaria cases in South Korea. When compared to isolates from other regions in the world, the amino acid sequences of the Korean isolates showed unique variations in region II. From 606 sequenced amino acids, 32 variations were found. Of these, three variations were regularly found in positions 424, 437 and 503 of the Sal-1 amino acid sequence. In region III, six isolates had a loss of the 30 bp (FAESTKSAE) insert. However, six isolates had 6 bp (SD) inserts at the end of region III. Two cases had a reverse pattern. Our results suggest that the P. vivax currently found in South Korea are unique when compared to other isolates and can be divided, by the analysis of their molecular structure, into two strains.