An automatic seedling transport system has been developed in order to improve the efficiency of seedling production, and to reduce the handling labor. The factory automation duct system was used to provide the power source and signal transmission. The seedling transport system has six functions: seedling inflow, seedling outflow, irrigation, pesticide application, tank rinse and re-location. The transport system integrates seeding system and basket-fitting system into a complete operation line for seedling production, where only two operators are needed. The system can be monitored and controlled through a computer in a remote control room.