MicroRNAs are 18-24nt small RNA species, which are known to regulate gene expression by repressing translation. The role of miRNAs were implicated in my biological processes such as embryogenesis, stem cells and cancer. In current study, we identified severa miRNAs that are enriched in the stem cells and the regenerating tissue of planarians. We also showed the role of microRNA, miR-124 in brain patterning in planaria. We also developed pipeline to analyze the targets of microRNAs, which will help to understand the functional role of miRNAs during planarain regeneration.