Feather pecking (FP) behavior causes restrictions on animal welfare and is associated with reduced performance, increments in mortality, and economic losses. This study aims to characterize the microbial communities of the ileum and the caecum of laying hens with feather pecking behavior and to establish an interaction with the conduct of high and low feather pecking. A white Leghorn laying hens line was divergently selected for FP for 15 generations, resulting in high feather pecking (HFP) and low feather pecking line (LFP). At 35 weeks after hatching, 95 birds were euthanized (49 HFP and 46 LFP), and samples from digesta and mucosa for both ileum and caeca were collected. DNA was extracted and subjected to target amplicon sequencing. Phylogenetic analysis was assessed using Qiime, followed by multivariate statistical analysis to establish interactions between the operational taxonomic units (OTUs) and HFP and LFP behavior. A significant effect on the microbiota was observed in the interaction between the section and feather pecking behavior (P <0.05). Ileum samples have lower bacterial diversity in comparison to caeca samples, being the lowest values observed for ileum mucosa samples. In ileum digesta, positive correlations were observed between body weight gain (BWG) and some of the most abundant OTUs. Ileum digesta showed an increase in the abundance of Firmicutes and the genus Lactobacillus in LFP. Ileum mucosa promoted Proteobacteria and Fusobacteria in HFP. Escherichia was detected in high abundance in HFP, while other beneficial microorganisms colonized the gut of LFP. In the caeca of digesta and mucosa samples, Faecalibacterium, Blautia, and unclassified Bacteroidales were present in higher abundance in LFP. Cecal microbiota does not drive an effect on BWG.Thus, not the same OTUs as in the ileum caused those correlations, making it difficult to establish the main bacterial drivers of BWG. This study clearly showed that the microbiota composition is associated with feather pecking activity.