The polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) technique is often used in laboratories and many basic research studies of complex genetic diseases associated with single nucleotide polymorphisms (SNP). When performing PCR-RFLP for SNP genotyping, feasible primer pairs are subject to numerous constraints and require a restriction enzyme for discriminating the target SNP. In this study, we develop a method for natural PCR-RFLP primer design for SNP genotyping using a particle swarm optimization algorithm. The in silico simulation with SNPs of the SLC6A4 gene demonstrates that this method reliably produces designs for natural PCR-RFLP primers which best fit the common primer constraints and also identifies available restriction enzymes.