[Objective] Plant ploidy identification is the basis for research on biological problems such as classification and ploidy breeding. Ploidy identification of complex ploidy species has been the focus of researchers" attention. That identification has become a difficult task especially for plants with a large number of chromosomes, small morphology, dense cytoplasm, and complex chromosome ploidy of species within the genus, and it is of great importance to explore a rapid and effective ploidy identification method. [Methods] In this study, young leaves of different plants in the genus Kiwifruit were used as material for ploidy identification using two methods - flow cytometry and single nucleotide polymorphism (SNP) loci heterozygous allele depth ratio (HADR) distribution. We explored the factors affecting ploidy identification, such as the growth status of the sampled leaves, the concentration of PVP (polyvinylpyrrolidone), the number of filter mesh and the number of filters, and the adjustment of parameters for whole-genome SNP typing of different ploidy samples. [Results] The highest number of intact nuclei was obtained by taking unexpanded young leaves in the flow cytometry assay; a 5% PVP concentration was the most suitable for reducing the adhesion between nuclei, 2% was not effective, and 7% caused no significant change. The 500 mesh filter used three times gave the best results; more impurities were found after the use of the 200 mesh and 300 mesh filtrations. SNP genotyping is mainly related to the quality of the assembly of the simulated genome and the parameter settings for filtering the identified SNPs. [Conclusion] The use of young unexpanded leaves to ensure a sufficient number of intact nuclei and reduce the adhesion between nuclei is the key to ploidy identification by flow cytometry. Chromosome ploidy of the same plant material did not change before and after CO60 the irradiation treatment. The assembly of high quality reference genome is the basis of SNP typing and the guarantee of heterozygote frequency distribution estimation at SNP loci. The results of the 2 ploidy identification methods in ploidy complex plants were consistent and could be validated against each other.