The morphology of 18 and seven species of fungi isolated from spoiled bean sprouts of Vigna spp. and soybean in Japan were respectively described, and DNA barcode markers of most isolates were sequenced to confirm the morphological identification. Fifteen and five species were isolated for the first time from Vigna spp. and soybean sprouts, including their ingredient grains, respectively. Globisporangium ultimum var. ultimum was newly recorded from the mung bean and most isolated fungi seemed to originate from the grains. Approximately 70% of isolates are recognized as plant pathogens and at least 14 species are known to be seed-borne. Inoculation experiments with representative strains of each species are needed to estimate the risks to bean sprout production and crop protection. Some strains of Fusarium graminearum isolated from the soybean were already reported as producing high concentrations of deoxynivalenol. Aspergillus flavus, which was found in mung bean sprouts, is a well-known aflatoxin producer. The ingredient grains should be imported after complete sterilization to avoid hazards; not only to bean sprout production but to human health. The effects of previously used sterilization techniques should be re-examined with the strains of various fungi isolated in this study to make them more practical.