• The rapidly developing fields of single-cell genomics and epigenomics provide powerful approaches to dissect cell heterogeneity in plants.

• The sensitivity and specificity of detecting single-nucleotide variations and copy-number variations via single-cell whole-genome amplification technologies have been continuously improving over the past decades. Recent applications highlight their feasibility and utility in plant single-cell genomics.

• Recent technical advances in single-cell epigenomics have enabled comprehensive and accurate profiling of diverse epigenomic features. The cell-specific epigenome facilitates the dissection of molecular mechanisms underlying biological processes in plants.

• Overcoming current technical issues and integrating multiomic single-cell sequencing data in plants will provide far greater understanding of plant functional genomics.

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