Mungbean is a kind of crop with strong resistance, and wide adaptability. The genetic diversity analysis and fingerprint analysis of all samples were detected using 19 polymorphic and stable core markers. The effective alleles of the InDel markers were between 1.100 and 1.996, with an average of 1.750. The expected heterozygosity (He) was between 0.0918~0.5049, with an average of 0.421. The variation of Nei"s gene diversity index was between 0.0907~0.4989, with an average of 0.416. The value of the polymorphic information content (PIC) was between 0.0866~0.3744, and 0.25 < 0.50 was the medium polymorphic. The average PIC content of InDel markers used in this experiment was 0.325. Using UPGMA to construct the clustering tree of 42 varieties of mungbean germplasm resources and the result showed that, 42 mungbean varieties (lines) could be divided into 2 groups while the genetic similarity coefficient is 0.55. Genetic analysis showed that the germplasm resources of the domestic mungbean have been isolated from the effect of regional isolation. By using 19 InDel markers, the DNA fingerprint of 42 cultivars of mungbean was constructed and 42 varieties of mungbean could be distinguished and accurately identified. The bands of InDel markers are easy to read in this study and they are suitable for DNA fingerprinting. Our results provide scientific basis for the identification of varieties, the protection of varieties of mungbean and provenance management.