Chloroplast genomes play a crucial role in sustaining life on Earth by converting solar energy into carbohydrates through photosynthesis. The availability of over 800 sequenced chloroplast genomes from various land plants has enhanced understanding of chloroplast biology, gene transfer, conservation, diversity, and the genetic basis for engineering chloroplast transgenes to improve plant traits or produce high-value products. This review discusses the impact of chloroplast genome sequences on understanding the origins of economically important species and changes during domestication, as well as their biotechnological applications. Chloroplast genomes are essential for understanding plant evolution, phylogenetics, and domestication. They have been used to identify commercial cultivars, determine purity, and improve breeding programs. Chloroplast genome sequences have also been used to study the evolutionary relationships and domestication history of major crops like rice, cotton, and legumes. The structure of chloroplast genomes is highly conserved, with a quadripartite structure including two copies of an inverted repeat (IR) region that separates large and small single-copy (LSC and SSC) regions. Chloroplast genomes contain 120–130 genes, primarily involved in photosynthesis, transcription, and translation. Advances in sequencing technologies have enabled rapid progress in chloroplast genomics. Next-generation sequencing (NGS) and third-generation sequencers like PacBio have facilitated the assembly of complete chloroplast genomes. Chloroplast genome sequences have revealed considerable variation in sequence and structure among plant species, providing insights into climatic adaptation and breeding. The use of chloroplast genomes in biotechnology includes conferring resistance to biotic and abiotic stress, developing vaccines and biopharmaceuticals in edible crops, and enhancing biomass production. Chloroplast genome engineering has been used to introduce foreign genes into the chloroplast genome, resulting in high levels of gene expression and reduced transgene escape. The integration of transgenes into intergenic spacer regions has been optimized to achieve homoplasmy and enhance transgene expression. Regulatory sequences, such as the psbA promoter, have been used to enhance transgene expression in photosynthetic organs. Heterologous regulatory sequences are necessary for transgene expression in non-photosynthetic organs. Chloroplast genomes have been engineered to produce useful enzymes, biomaterials, and biofuels, or to enhance biomass. The first report of metabolic engineering using chloroplast genomes produced high levels of poly(p-hydroxybenzoic acid) polymer. Chloroplast-derived enzyme cocktails offer advantages such as reduced cost, improved stability, and no need for enzyme purification. The expression of β-glucosidase released hormones from conjugates, resulting in elevated phytohormone levels and increased biomass. Chloroplast genomes have also been used to enhance nutrition by modifying seed oils to increase the levels of vitamin E. Seed oils from soybean, rapeseed, and maize are major dietary sources of vitamin E, with varying levels ofChloroplast genomes play a crucial role in sustaining life on Earth by converting solar energy into carbohydrates through photosynthesis. The availability of over 800 sequenced chloroplast genomes from various land plants has enhanced understanding of chloroplast biology, gene transfer, conservation, diversity, and the genetic basis for engineering chloroplast transgenes to improve plant traits or produce high-value products. This review discusses the impact of chloroplast genome sequences on understanding the origins of economically important species and changes during domestication, as well as their biotechnological applications. Chloroplast genomes are essential for understanding plant evolution, phylogenetics, and domestication. They have been used to identify commercial cultivars, determine purity, and improve breeding programs. Chloroplast genome sequences have also been used to study the evolutionary relationships and domestication history of major crops like rice, cotton, and legumes. The structure of chloroplast genomes is highly conserved, with a quadripartite structure including two copies of an inverted repeat (IR) region that separates large and small single-copy (LSC and SSC) regions. Chloroplast genomes contain 120–130 genes, primarily involved in photosynthesis, transcription, and translation. Advances in sequencing technologies have enabled rapid progress in chloroplast genomics. Next-generation sequencing (NGS) and third-generation sequencers like PacBio have facilitated the assembly of complete chloroplast genomes. Chloroplast genome sequences have revealed considerable variation in sequence and structure among plant species, providing insights into climatic adaptation and breeding. The use of chloroplast genomes in biotechnology includes conferring resistance to biotic and abiotic stress, developing vaccines and biopharmaceuticals in edible crops, and enhancing biomass production. Chloroplast genome engineering has been used to introduce foreign genes into the chloroplast genome, resulting in high levels of gene expression and reduced transgene escape. The integration of transgenes into intergenic spacer regions has been optimized to achieve homoplasmy and enhance transgene expression. Regulatory sequences, such as the psbA promoter, have been used to enhance transgene expression in photosynthetic organs. Heterologous regulatory sequences are necessary for transgene expression in non-photosynthetic organs. Chloroplast genomes have been engineered to produce useful enzymes, biomaterials, and biofuels, or to enhance biomass. The first report of metabolic engineering using chloroplast genomes produced high levels of poly(p-hydroxybenzoic acid) polymer. Chloroplast-derived enzyme cocktails offer advantages such as reduced cost, improved stability, and no need for enzyme purification. The expression of β-glucosidase released hormones from conjugates, resulting in elevated phytohormone levels and increased biomass. Chloroplast genomes have also been used to enhance nutrition by modifying seed oils to increase the levels of vitamin E. Seed oils from soybean, rapeseed, and maize are major dietary sources of vitamin E, with varying levels of