Microsatellites, namely simple sequence repeats (SSR), are simple tandemly repeated sequences with repeat units of 1-6 bp in length. As genetic markers, microsatellites are abundant and distributed throughout the eukaryotic genomes. Their advantages include high polymorphism and abundance, co-dominance, selective neutrality and high reliability. In recent years, microsatellite markers are often used to study the biologically genetic diversity. In this paper, we briefly review the application of microsatellite technique in the study of Plasmodium spp. genetic diversity.