MicroRNAs (miRNAs) are 21-23 nucleotide (nt) long non coding post-transcriptional regulators of gene expression. In vitro propagation to enhance production of high yielding, disease-free planting material in coconut has remained a distant reality since coconut is recalcitrant to in vitro culture. In order to decipher the mechanisms controlling somatic embryogenesis in coconut, we have carried out small RNA sequencing of embryogenic (EC) and non-embryogenic calli (NEC) of coconut using high-throughput Illumina HiSeq2000 platform.