Advances in next-generation sequencing (NGS) have transformed plant genomics by enabling high-resolution analysis of genome structure, function, and evolution. This chapter provides a thoughtful review of the development of first-, second-, and third-generation sequencing platforms, the principles on which they are based, technological advancements, and potential developments in plant science. The chapter outlines how successive sequencing generations have progressively improved genome assembly quality, gene expression profiling, variant discovery, and the detection of epigenetic modifications. Key applications, including whole-genome sequencing, RNA–Seq, SNP discovery, epigenome analysis, and integrative multi-omics approaches, are the dominant themes, showing how genomics can fold with proteomics, metabolomics, and phenomics. Moreover, case studies and examples demonstrating the potential of NGS in both model and non-model plant species are included to illustrate its utility in addressing complex biological questions, advancing crop improvement, and supporting conservation efforts. While describing challenges of polyploidy, repetitive DNA, data management, and bioinformatics bottlenecks, future advances in the field, and artificial intelligence datasets are also included.