Large-scale seedling production aims to improve their production capacity and competitiveness by improving productivity, reducing labour costs, and eliminating labour-intensive production processes. With the pursuit of continuously improving productivity, the development of automatic seedling production has become a key technology. However, achieving the automatic separation of rootless collected seedlings into individual plants remains an important challenge because tender rootless seedlings need to be separated into individuals for feeding into seedling production equipment. In this study, a separator composed of subdivided air streams was developed to separate tender collected seedlings into individuals. The air streams for separation were generated by a jetting nozzle array of subdivided air streams at the base of the separator. By opening and closing different subdivided air stream nozzles, in turn, seedlings became suspended with some seedlings at the edge of the floating mass becoming separated. The separator was tested using aubergine and cucumber seedlings intended for grafting and for anthurium seedlings intended for cuttage transplanting. The results demonstrated that the separator could separate tender collected seedlings into individuals without causing damage. Moreover, the maximum separation rates for the collected seedlings were 11,070, 13,590, and 17,100 plants per hour for the aubergine, cucumber, and anthurium seedlings, respectively.