Various Lycopodium alkaloids have been studied for their various biological activities including anti-inflammatory, antioxidant, immunomodulatory, and neuroprotective activities. Moreover, these alkaloid compounds have high potential in the treatment of neuron degenerative disease. This study has been carried out to test the effect of Huperzia serrata (Thunb.) Trevis, and Lycopodium clavatum L alkaloid fractions on the mouse neural stem cells (NSCs). Firstly, the alkaloid fractions were used to verify its toxicity on NSCs. The multiple concentrations of alkaloid fractions from H. serrata (0.044; 0.088; 0.175; 0.35; 0.7; 1.4 mg/ml) and L. clavatum (0.031; 0.063; 0.125; 0.25; 0.50; 1.0; 2.0 mg/ml) have been used for the treatment of NSCs at period of 48h incubation. Results of the study suggested that the IC50 value of H. serrata and L. clavatum was 0.56 mg/ml and 0.50 mg/ml, respectively. Then, the NSCs were differentiated in the presence of 5 and 10 µg/ml of alkaloid fraction from H. serrata; 0.625 and 1.25 µg/ml of alkaloid fraction from L. clavatum for 6 days. Here, we observed the primary NSCs treated with alkaloid fraction extract from H. serrata showed the increased gene expression level of early neuron TUBB3 and neuron-specific cytoskeleton MAP2. On the other hand, the L. clavatum alkaloid fraction increased the expression of neural stem cell marker genes (Nestin and PAX6) and decreased neuron marker genes. In conclusion, these results established that alkaloid fraction from H. serrata promoted differentiation of the mouse NSCs to neuron cells, and L. clavatum extract had a capacity for stemness maintenance.