Among the models that are available to plant scientists for studying the impact of epigenetic regulations on agronomically and economically relevant crop phenotypes, the mantled somaclonal variation of the oil palm is one of the oldest, since its association with genome-wide hypomethylation has been established >20 years ago. Since then, significant progress has been made towards elucidating the molecular mechanisms of floral organ feminization in adult plants generated through somatic embryogenesis. Yet, to this day, the origin of this variant phenotype during early stages of the in vitro process remains to be identified, and thus the reliable assessment of clonal phenotype stability still elude us. In order to better understand the epigenetic misregulations involved in the emergence of the mantled phenotype, we are currently investigating the role of small non-coding RNAs (sncRNAs) in embryogenic suspensions of oil palm using high-throughput sequencing techniques. During a first phase of the project, we profiled the different size classes of sncRNAs produced in different embryogenic lines. We then used in silico prediction software to identify likely target transcripts of sequenced microRNAs (miRNAs), some of which were subsequently validated by 5'RACE. A comprehensive degradome analysis is also under way, and will provide us with a comprehensive overview of small RNA-mediated post-transcriptional regulation mechanisms under our experimental conditions. We will discuss our results and their implications with respect to the study of epigenetic regulations in non-model crop genomes.