The zygotic genome becomes activated soon after plant fertilisation, and cells rapidly adopt distinct transcriptional programmes to drive differentiation. Although whole-embryo transcriptome studies have uncovered some of the gene expression dynamics that drive this cellular diversification, this approach lacks cellular resolution and carries the risk of maternal RNA contamination; newer single cell sequencing technologies are also currently impractical due to the embryo's rigid cell walls. Now, Ping Kao, Michael Schon, Michael Nodine and colleagues surmount these problems by coupling fluorescence-activated nuclei sorting with single-nucleus mRNA-sequencing (snRNA-seq) in the Arabidopsis embryo. Driving nuclear-localised GFP only in cells of the embryo, and not in the surrounding endosperm or maternal tissues, allows for efficient isolation of embryonic nuclei and subsequent construction of hundreds of high-quality snRNA-seq libraries. By supervised clustering, comparison with previous transcriptomes and RNA in situ hybridization, the authors then efficiently assign these libraries to nine known major cell types in globular embryos. Expression of epigenetic regulators varies among the different embryo cell types – indicating, for example, that DNA methylases become preferentially activated in the basal cell lineage. Finally, the authors characterise the enrichment of different transcription factor-binding motifs in the most highly expressed genes in each cluster. This article thus presents both a technical advance and a valuable resource for plant embryologists.