Background Somatic embryogenesis receptor-like kinase 1 (SERK1) is a cell membrane receptor active in different plant tissues and involved in cell differentiation activities including somatic embryogenesis. The identification of promoter elements responsible for SERK1 expression during the onset of somatic embryogenesis can be useful to understand the molecular regulation of the cell-to embryo transition, and these promoter elements represent biotechnological tools in plant organ tissue culture. Results A − 1,620 bp DNA sequence located upstream of the Coffea canephora SERK1 gene homologue (CcSERK1) was isolated, and then, different segments containing key response elements (REs) for somatic embryogenesis onset and development were fused to the uidA (encoding a β-glucuronidase, GUS) reporter gene to evaluate its expression in transgenic leaf explants. DNA segments of − 1,620 and − 1048 bp in length directed uidA expression with patterns in leaf explants similar to those occurring during somatic embryogenesis. When a − 792-bp fragment was used, uidA expression disappeared only in leaf explants and pro-embryogenic mass but persisted in developing embryos. No uidA expression was detected in any embryogenic stage when a − 618-bp fragment was used. Conclusion DNA deletions showed that a − 1048-bp sequence located upstream of the CcSERK1 gene is sufficient to direct gene expression during the onset and the development of C. canephora somatic embryogenesis. The DNA segment located between − 1048 and − 792 bp (containing BBM and WUS REs) is needed for gene expression before embryogenesis onset but not during embryo development. The promoter segment between − 792 and − 618 bp (including GATA, ARR1AT, and ANT REs) regulates gene expression in developing embryos. How to cite: Jiménez-Guillen D, Pérez-Pascual D, Souza-Perera R, et al. Cloning of the Coffea canephora SERK1 promoter and its molecular analysis during the cell-to-embryo transition. Electron J Biotechno