Regulatory non coding RNAs, including microRNAs (miRNAs) and long non coding RNAs (lncRNAs), have shown to be essential for animal development and viability, yet dissecting the relevance of individual miRNA or lncRNA has been challenging for a given cell context. In addition, the role of ncRNAs for neurodegeneration is still obscure. To identify ncRNAs participated during motor neuron development and degeneration, we used human embryonic stem cell and motor neuron disease iPSCs as paradigms and robustly harnessed them into different motor neuron subtypes to perform strand specific RNA-seq and small RNA-seq simultaneously. We identified several novel MN signature miRNAs and lncRNAs, and systematically analyzed their functions by generating knockout mice. I will present the current progress of the characterization of these MN-ncRNAs by gain-of-function and loss-of-function studies. Collectively, these results will provide critical information for ncRNAs function and will fill in the information on how ncRNAs mediate MN development in vivo.