<p>Coconut is a perennial crop with immense economic and social importance; however, the lack of efficient in vitro propagation techniques constrains its large-scale production. Current propagation methods fail to meet the rising demand for high-quality, disease-resistant palms. Somatic embryogenesis (SE) offers a viable alternative by enabling the production of genetically uniform clones of desirable varieties. Nonetheless, applying SE in coconut remains challenging due to its inherent recalcitrance. A deeper understanding of the molecular mechanisms governing SE and the factors regulating it is essential to enhance tissue culture protocols. This study examines the role of microRNAs (miRNAs) and their target genes at various stages of zygotic embryogenesis (ZE) and SE in coconut. Through quantitative real-time PCR (qRT-PCR), the expression patterns of five conserved miRNAs—cnu-miR166a, cnu-miR167c, cnu-miR169a, cnu-miR171a and cnu-miR397 and their targets, which are involved in processes such as transcriptional regulation, hormone signalling, and cell wall development were analysed. The findings revealed distinct expression patterns of these miRNAs at different stages of embryogenesis. Specifically, cnu-miR166a and cnu-miR167c were predominantly expressed during early ZE, while cnu-miR169a and cnu-miR397 exhibited significant upregulation during SE. The inverse relationship observed between most miRNAs and their target gene expression highlights their regulatory significance in embryogenesis. Downregulation of cnu-miR169a and cnu-miR397 via short tandem target mimics could be a viable strategy to obtain the desired SE potential in coconut. This study provides fundamental insights into the miRNA-driven regulatory network during SE in coconut, offering potential avenues for optimizing propagation techniques and improving tissue culture outcomes.</p>