Sequence analyses on the intron from the elongation factor-1α gene were conducted to examine the population structure of sword prawn (Parapenaeopsis hardwickii) in the East China Sea and Taiwan Strait. Five samples including 207 individuals were separately collected from the north of East China Sea (NECS) and waters off Tamsui, Taichung, Putai, and Cheding, and 102 alleles were identified. Despite no phylogeographic structure in alleles, pairwise F_ST values and analysis of molecular variance (AMOVA) showed significant genetic difference between the NECS and the other four samples. The UPGMA tree of five samples showed two distinct clusters; one included the NECS sample; the other included the rest of samples. The results suggest that two populations exist in the East China Sea and Taiwan Strait. To ensure resource sustainability and maintenance, the sword prawn in the Taiwan Strait and the north of the East China Sea should be treated as two separate populations and then be separately managed in future. Both Tajima's D and Fu and Li's D statistics and analysis of mismatch distribution for overall alleles suggested that sword prawn in studied area had experienced population expansion.