Abstract: Compared to animals and microorganisms, the application of flow cytometry for plant science is quite difficult in regards to sample preparation, dyeing and testing, which can lead to failure in detection or inaccurate results, due to the special structures and ingredients of plant material (e.g., cell walls, central vacuoles, multifarious organelles and secondary metabolites). Through long-term use of flow cytometry and reference to related literature, we accumulated significant experience in plant science, especially in specimen collection, sample preparation and nuclear DNA content detection. Accordingly, this report provides a valuable reference for plant science and technical personnel engaged in flow cytometry testing.