Raw milk of cows fed with silage or hay was used for Caciocavallo cheeses manufacture. rRNA high-throughput sequencing revealed in-depth the microbiota of Caciocavallo. Streptococcus thermophilus was the dominant species in both silage and hay cheeses. Differences in the microbiota of milk within diet groups were not related to cows' feeding. Feeding and ripening time influenced cheese attributes.