Whole crop corn silage may be prone to spoilage after exposure to air. To investigate control of fermentation and aerobic spoilage by using silage additives, Lactobacillus rhamnosus and Lactobacillus buchneri were added to whole crop corn silage, and shifts in microbial communities were examined. Bacterial and fungal communities were identified by denaturing gradient gel electrophoresis analysis at the time of opening the silo and after conducting aerobic deterioration tests. Inoculation of L. rhamnosus did not affect fermentation, whereas that of L. buchneri decreased the lactic acid content and increased the acetic acid content. Aerobic stability was enhanced in silage stored for a long period (120 days), with increases in the acetic acid content even without L. buchneri inoculation. A high aerobic stability was achieved with a shorter ensiling period (56 days) in L. buchneri-inoculated silage. Lactic acid bacteria (LAB) inoculation did not alter the indigenous bacterial community, and the inoculated species were detected only as additions. Lactobacillus brevis, Pediococcus parvulus, Weissella confusa and Klebsiella pneumoniae were found in both the pre-ensiled crop and the silage, whereas Weissella paramesenteroides, Lactobacillus plantarum and Lactobacillus lactis were seen exclusively after ensiling. Inoculation also had little effect on the fungal community during the fermentation process. Candida magnolia, Cryptococcus flavus and Candida intermedia were detected, both in the pre-ensiled crop and the silage, whereas Candida glabrata and Candida quercitrusa were identified exclusively in the silage. Marked changes were seen in the fungal community after aerobic spoilage; Saccharomyces exiguus, Saccharomyces martiniae, Pichia fermentans, Pichia deserticola and Pichia kudriavzevii appeared in the spoiled silage. These results indicated that LAB inoculation produces few changes in bacterial and fungal communities in corn silage and that substantial changes occur in the fungal community when the silage is spoiled.