Microsatellite markers, composed of short tandem repeats of two to six nucleotides, are widely distributed in the genomes of eukaryotes. Their characteristics, including high levels of polymorphism, abundance,adherence to Mendelian inheritance laws, and ease of amplification via polymerase chain reaction, have made them the most commonly employed method for paternity testing in non-human primates. Abundant primate species represent invaluable genetic resources worldwide; however, the quantity and productivity of primate genetic resources have declined as a result of habitat destruction, illegal hunting, the pet trade, and inadequate protection and management.Research into primate conservation using molecular technologies has thus become a mainstream approach to protect primate species. This review systematically considers the structural characteristics and genetic properties of microsatellite markers and clarifies their advantages and limitations, thereby providing a theoretical basis for the rational selection of research tools in subsequent studies. We detail the significance of microsatellite markers in nonhuman primate research, as well as their applications in parentage identification in captive populations and the genetic assessment of wild populations. These applications demonstrate that microsatellite markers can accurately identify parentage, effectively avoid inbreeding, and safeguard population genetic diversity. They can also provide scientific data to support the formulation of species-conservation strategies through the assessment of indicators such as genetic diversity levels and gene flow. Finally, by integrating the current research status, this study discusses the existing limitations and challenges to the development of microsatellite markers, and the prospects for their future development by combining with next-generation sequencing and multi-omics technologies. This review thus provides scientific support for the population management of primates, the conservation of species diversity, and future related developments.