It was evaluated the impacts caused by microbial inoculants on the fungal population of rehydrated corn and sorghum grain silage by Internal transcribed spacer region (ITS) rRNA Illumina MiSeq sequencing. A 2 × 3 × 6 factorial scheme was used, with 2 grains (corn, CG; sorghum, SG), 6 fermentation periods (0, 3, 7, 21, 90 and 360 d) and 3 inoculants: CTRL, non-inoculated; Inoc1, Lactobacillus plantarum and Propionibacterium acidipropionici (Lalsil Milho, Lallemand Animal Nutrition) and Inoc2, Lactobacillus buchneri (Lalsil AS, Lallemand Animal Nutrition), with 3 replicates in a completely randomized design. The phyla Ascomycota was predominantly found in both grains silages followed by small abundance of Basidiomycota and Mucoromycota. Aspergillus spp. represented 51–89% of the initial population of CG samples. In CG-CTRL silages as early as 3 d it was observed a sharp growth of Wickerhamomyces (60%) yeasts which extended up 21 d of fermentation. After, Aspergillus returned to dominate from the 90 d until the end of the fermentation. Similar response was observed in CG-Inoc2 silages. Bacteria present in Inoc1 resulted in fermentation with the predominance of Aspergillus genus up to 90 d. However, at 360 d, 86% of the genera were represented exclusively by unidentified yeasts belonging to the order Saccharomycetales. Greater participation of different genera were observed in initial samples of SG than CG. Alternaria accounted for 30–60% of the initial population of the SG which were replaced by Wickerhamomyces anomalus in the intermediate periods of fermentation. Aspergillus spp. were predominant in rehydrated corn grain fermentation while W. anomalus was the major fungal in rehydrated sorghum grain silages. The addition of microbial inoculants did not have an influencial effect on fungal population of rehydrated sorghum grain silages, while the mix of L. plantarum and P. acidipropionici controled the growth of Wickerhamomyces yeast until 90 d of fermentation in rehydrated corn grain silages. Supported by CNPq, CAPES, and INCT-CA