To investigate the effect of overfeeding on the ileal and cecal microbiota of two genotypes of ducks (Pekin and Muscovy), high-throughput 16S rRNA gene-based pyrosequencing was used. The ducks were overfed for 12days with 58% maize flour and 42% maize grain. Samples were collected before the overfeeding period (at 12weeks), at 13weeks, at 14weeks, and 3h after feeding. In parallel, ducks fed ad libitum were killed at the same ages. Whatever the digestive segment, the genotype, and the level of intake, Firmicutes and Bacteroidetes are the dominant phyla in the bacterial community of ducks (at least 80%). Before overfeeding, ileal samples were dominated by Bacilli, Clostridia, and Bacteroidia classes (70%), and cecal samples, by Bacteroidia and Clostridia classes (around 90%) in both Pekin and Muscovy ducks. The richness and diversity decreased in the ileum and increased in the ceca after overfeeding. Overfeeding triggers major changes in the ileum, whereas the ceca are less affected. Overfeeding increased the relative abundance of Clostridiaceae, Lactobacillaceae, Streptococcaceae, and Enterococcaceae families in the ileum, whereas genotype affects particularly three families: Lachnospiraceae, Bacteroidaceae, and Desulfovibrionaceae in the ceca.