Chloroplasts play a crucial role in sustaining life on Earth through photosynthesis and other metabolic processes. The availability of over 800 sequenced chloroplast genomes from various land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis for engineering chloroplast transgenes to enhance plant agronomic traits or produce high-value agricultural or biomedical products. This review discusses the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes during domestication. It also highlights the potential biotechnological applications of chloroplast genomes, such as conferring protection against biotic or abiotic stress and the development of vaccines and biopharmaceuticals in edible crop plants. Advances in chloroplast genome sequencing technology, including next-generation sequencing (NGS) and third-generation sequencing, have facilitated rapid progress in chloroplast genomics. The structure of chloroplast genomes is highly conserved, but there is variation in sequence and structural content. Complete chloroplast genome sequences are valuable for phylogenetic studies and improving our understanding of plant evolution. Chloroplast genome engineering has been used to introduce desirable traits from unrelated species into commercial cultivars, with high levels of transgene expression and maternal inheritance minimizing transgene escape via pollen. The selection of suitable intergenic spacer regions and regulatory sequences is crucial for efficient transgene integration and expression. Recent applications of chloroplast genome engineering include conferring stress tolerance, synthesizing enzymes and biomaterials, enhancing nutrition, and producing biopharmaceuticals, demonstrating the potential of this technology in agriculture and biotechnology.Chloroplasts play a crucial role in sustaining life on Earth through photosynthesis and other metabolic processes. The availability of over 800 sequenced chloroplast genomes from various land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis for engineering chloroplast transgenes to enhance plant agronomic traits or produce high-value agricultural or biomedical products. This review discusses the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes during domestication. It also highlights the potential biotechnological applications of chloroplast genomes, such as conferring protection against biotic or abiotic stress and the development of vaccines and biopharmaceuticals in edible crop plants. Advances in chloroplast genome sequencing technology, including next-generation sequencing (NGS) and third-generation sequencing, have facilitated rapid progress in chloroplast genomics. The structure of chloroplast genomes is highly conserved, but there is variation in sequence and structural content. Complete chloroplast genome sequences are valuable for phylogenetic studies and improving our understanding of plant evolution. Chloroplast genome engineering has been used to introduce desirable traits from unrelated species into commercial cultivars, with high levels of transgene expression and maternal inheritance minimizing transgene escape via pollen. The selection of suitable intergenic spacer regions and regulatory sequences is crucial for efficient transgene integration and expression. Recent applications of chloroplast genome engineering include conferring stress tolerance, synthesizing enzymes and biomaterials, enhancing nutrition, and producing biopharmaceuticals, demonstrating the potential of this technology in agriculture and biotechnology.