Genotyping of Plasmodium falciparum based on PCR amplification of the polymorphic genes encoding the merozoite surface proteins 1 and 2 (msp1 and msp2) is well established in the field of malaria research to determine the number and types of concurrent clones in an infection. Genotyping is regarded essential in anti-malarial drug trials to define treatment outcome, by distinguishing recrudescent parasites from new infections. MSP-1 is the major surface antigen of merozoites and is the best-studied protein. During the invasion process, several proteins of the 195-KDa MSP-1 are shed, leaving a highly conserved 19 KDa C-terminal processing fragment (MSP-19) that contains epitopes targeted by antibodies that inhibit erythrocytic invasion. MSP-2 is a second merozoite surface antigen. It is smaller polypeptide with a molecular weight of 45 KDa that is processed during parasite maturation. The antibody response is directed almost completely towards variant regions of MSP-2. The conserved regions are rarely recognized. All samples screened for P.falciparum msp-1 alles, msp-2 alles by PCR. The results revealed that the overall Plasmodium falciparum detection rate between MSP-1&-2, PCR based genotyping of msp-1 allele showed that the rate of msp-2 was higher (53%) than msp-1(13%). Conclusion: We conclude that our finding might probably be attributed to strain differences, and or ethnic differences.