Background and Objectives: Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) is a promising vaccine against malaria during its blood stages which play an important role in immunity to this disease. Polymorphic nature of this gene is a major obstacle in making an effective vaccine against malaria. In this study, the genetic diversity of Plasmodium falciparum isolates was investigated in Sistan-Baluchestan Province using allelic families of the MSP-1. Methods: From March/April 2011 to August/September 2012, 94 blood samples were collected from patients with falciparum malaria who were living in four districts of Sistan-Baluchestan Province. The extracted genomic DNA and genetic diversity of MSP-1 block 2 were evaluated by nested polymerase chain reaction. Results: From a total of 94 patients, 89 patients (94.7%) had positive PCR results and the remaining five patients were excluded. Seven different alleles of MSP-1 were identified through size difference on agarose gel. Comprising 46.1% of the samples, MAD20 was identified as the predominant MSP-1 allelic family, while the RO33 family had the lowest frequency (with 7.9%). In 10% of samples infection with two alleles was observed. Conclusion: The results of this study suggest that genetic diversity of PfMSP-1 in Southeastern Iran is relatively low and most infections originate from a clone that is consistent with an area of low malaria transmission. This information is useful for the prevention and control of malaria in Iran.