Along with development of advanced molecular markers, the fate of plant biotechnology, plant breeding and genetic studies has changed. Mainly, there are various kinds of markers viz. morphological, biochemical and DNA based molecular markers. Among these markers’ DNA based molecular markers mainly used because of their abundances. Genetic markers play a significant role to find out genetic difference between different organism and species. In 20th century numerous DNA markers reported in published literature that have been utilized in plant breeding programs. The advancement in genomic studies has created a basic platform for designing breeding experiments and complete knowledge of molecular markers for diversity analysis in crops. Novel genetic markers were identified by Genotyping-by-sequencing and association mapping was performed with the help of next-generation sequencing technologies for a complex population. In this chapter altogether, the marker evolution history, markers classification, significance of markers, and genome editing and genomic selection advancement and some other advance methods are discussed.