With it's unprecedented through put, scalability and speed Next Generation Sequencing (NGS) enables researchers to study biological systems at a level never before. Recent advancement in NGS includes Nanopore DNA sequencing, Tunneling currents DNA sequencing, sequencing by hybridization, microscopy based techniques, micro fluidic Sanger sequencing, RNAP sequencing, in vitro virus high throughput sequencing etc. Next generation sequencing applies to genome sequencing, genome resequencing, transcriptome profiling (RNA-Seq), DNA protein interactions (chip sequencing) and epigenome characterization. NGS is applied in plant research for genotyping, crop improvement and for rapid marker development in molecular plant breeding. It is used for plant transcriptomics including gene discovery, transcript quantification and marker discovery for non model plants as well as transcript annotation and quantification, small RNA discovery and transcription analysis for model plants. NGS enables the collection of genome-wide information on genetic variation, single nucleotide polymorphism (SNP) markers and identification of genes of adaptive importance which will help considerably in investigating the mechanisms that are important in a conservation genetic context such as inbreeding depression and local adaptation.