The introduction of molecular markers in the latter part of the twentieth century denoted a major advancement in the research on plant genetics. Molecular markers have become highly advantageous to help overcome certain inherent difficulties associated with the genetic improvement of perennial crops such as coconut. Starting from the middle of the 1990s, considerable progress has been achieved in the genetic diversity analysis of coconut. The early attempts of molecular research on coconut used the common molecular marker systems of the time, such as randomly amplified polymorphic DNA and amplified fragment length polymorphism. Later, the generation of coconut-specific DNA markers and the adoption of high-throughput systems have paved the way for an acceleration, with greater accuracy, in using molecular markers for diversity studies in coconut. Molecular markers have also been used in the development of linkage maps and the identification of quantitative trait loci (QTL) in coconut. The research using molecular markers has been used, and will be further useful, in formulating and refining the further collection and conservation of coconut germplasm, the management of genebanks, identification of duplicates, and determining the strategies for rejuvenation of the existing field genebanks. The data can further be used in the parental selection in the coconut breeding programmes aimed at combining the desirable characters from diverse parents into novel cultivars. The availability of high-throughput marker systems will increase the accuracy and precision of genetic and QTL mapping via linkage analysis. Further, association studies which facilitate the use of existing populations in QTL mapping will be an important tool in moving towards marker-assisted selection of coconuts for desirable traits to ensure sustainability of the coconut industry.