Microsatellite markers, composed of short tandem repeats of 2～6 nucleotides, are widely distributed in the genomes of eukaryotes. Owing to their characteristics such as high polymorphism, abundance, adherence to Mendelian inheritance laws, and ease of amplification via polymerase chain reaction (PCR), they have become 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 due to habitat destruction, illegal hunting, pet trade, and inadequate protection and management. To fully protect primates, research on primate conservation using molecular technologies has become mainstream. This study systematically elaborates on the structural characteristics and genetic properties of microsatellite markers, clarifies their advantages and limitations, and thereby provides a theoretical basis for the rational selection of research tools in subsequent studies. On this basis, it details the significance of microsatellite markers in non-human primate research, as well as their applications in parentage identification of captive populations and genetic assessment of wild populations. These applications demonstrate that microsatellite markers can accurately achieve parentage identification, effectively avoid inbreeding, and safeguard population genetic diversity; furthermore, they can provide scientific data support for 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 in the development of microsatellite markers and prospects their development trend of combining with next-generation sequencing technology and multi-omics technology. The purpose of this study is to provide scientific support for the population management of primates, the conservation of species diversity, and future related development.