Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for studying plant systems and synthetic biology. Plants are complex organisms with diverse cell types, and scRNA-seq provides high-resolution insights into gene expression patterns and cell-type heterogeneity. This technology is particularly useful for understanding plant development, stress responses, and epigenetic regulation at the cellular level. It also has potential for designing and engineering plant traits through genome editing and synthetic biology approaches. scRNA-seq has been applied to various plant species, including model plants like Arabidopsis thaliana, agricultural crops like Oryza sativa, and bioenergy crops like Populus spp. Recent advancements in scRNA-seq include improved protocols for cell isolation, library preparation, and sequencing technologies, as well as computational tools for data analysis. Challenges remain, such as limited availability of plant cell atlases, difficulties in capturing rare cell types, and technical noise due to low RNA content. Despite these challenges, scRNA-seq is expected to play a key role in advancing plant systems biology and synthetic biology research. Future developments in scRNA-seq technology, including more cost-effective methods and integration with other omics approaches, will further enhance its application in plants. The development of standardized protocols and databases will be crucial for ensuring the reproducibility and comparability of scRNA-seq data across different plant species and research settings. Overall, scRNA-seq is a promising tool for uncovering the molecular mechanisms underlying plant biology and for engineering new plant traits.Single-cell RNA sequencing (scRNA-seq) has become a powerful tool for studying plant systems and synthetic biology. Plants are complex organisms with diverse cell types, and scRNA-seq provides high-resolution insights into gene expression patterns and cell-type heterogeneity. This technology is particularly useful for understanding plant development, stress responses, and epigenetic regulation at the cellular level. It also has potential for designing and engineering plant traits through genome editing and synthetic biology approaches. scRNA-seq has been applied to various plant species, including model plants like Arabidopsis thaliana, agricultural crops like Oryza sativa, and bioenergy crops like Populus spp. Recent advancements in scRNA-seq include improved protocols for cell isolation, library preparation, and sequencing technologies, as well as computational tools for data analysis. Challenges remain, such as limited availability of plant cell atlases, difficulties in capturing rare cell types, and technical noise due to low RNA content. Despite these challenges, scRNA-seq is expected to play a key role in advancing plant systems biology and synthetic biology research. Future developments in scRNA-seq technology, including more cost-effective methods and integration with other omics approaches, will further enhance its application in plants. The development of standardized protocols and databases will be crucial for ensuring the reproducibility and comparability of scRNA-seq data across different plant species and research settings. Overall, scRNA-seq is a promising tool for uncovering the molecular mechanisms underlying plant biology and for engineering new plant traits.