Alfalfa silage (Al) and corn silage (Cs) samples were collected from two large-scale farms in China; one of these farms used stack silos and the other used bunker silos for silage production. Three samples were collected from the upper and lower layers of each silo. Thus, six samples were examined for each of Al-stack, Al-bunker, Cs-stack, and Cs-bunker. Bacterial community was determined by denaturing gradient gel electrophoresis (DGGE). Lactic acid was the main fermentation product in Al-stack, Cs-stack and Cs-bunker, whereas acetic acid and butyric acid were predominant in Al-bunker. Pediococcus pentosaceus and Clostridium sp. were common to four silage types. Lactobacillus acetotolerans and Lactobacilluspontis were detected specifically in Cs, whereas the lactic acid bacteria identified in Al were regarded as those usually found in silage. Differences between stack and bunker silos were apparent in Al with regard to fermentation products and DGGE band patterns. Differences between the upper and lower layers were observed in the fermentation products in Cs regardless of silo type, whereas variations in the DGGE band patterns of Cs-stack were detected.