Genetic advancement in various crop plants is hindered due to their complex genome, substantial heterozygosity, and self-incompatibility. However, maintenance of genetic resources and germplasm of crop plants depends largely on mankind’s ability to comprehend genetic diversity. In recent time, improvement in various sequencing techniques and emergence of molecular markers has altered the plant breeding outcomes. To foster crop improvement, various kinds of molecular markers have been produced, as they provide a way to unveil genetic variability. In spite of their simplicity, they are highly reproducible, ensuring precise estimations of plant diversity. Integrating different marker approaches with cutting-edge high throughput sequencing methods poised to improve our knowledge and ability to manage the diminishing plant genetic resources by imparting an entire picture of genome-wide diversity. These markers have been generated and mapped for various crop plants in order to look at phylogenetic linkages and genetic diversity for the utilization and protection of genetic resources. This chapter can act as an itinerary for implementing most effective marker approaches to analyze different crop plants in near future.