Paddy rice has been of particular interest as a forage crop in Japan. In this study, the isolated strains TO1000, TO1001, TO1002, and TO1003 were characterized by phenotypic and genotypic approaches. These strains were identified as Lactobacillus plantarum subsp. plantarum by species-specific PCR. Phenotypic characteristics varied among different strains of the same subspecies, and the strains represented unique and diverse phenotypes related to fermentation factors, such as carbohydrate assimilation and range of pH and temperature allowing growth. PCR analysis revealed that the patterns of presence/absence of known plantaricin genes differed in a strain-specific manner. Using these strains as inoculants for preparation of whole crop paddy rice silage, fermentation quality was significantly improved, as shown by lower pH, higher lactic acid content, and inhibition of the growth of undesirable microorganisms such as molds, coliform bacteria, and clostridia, after 30 and 60 days of storage, with effectiveness differing from strain to strain. These observations suggest that suitable candidates for bacterial inoculants in silage preparation should be screened at the strain level. Strain TO1002 may be useful for producing silage inoculants for the production of well-preserved whole crop paddy rice silage.