The composition of the gastrointestinal microorganisms in poultry is closely associated with the host and its environment. In this study, using 16S rRNA and metagenomic techniques, we comprehensively analyzed the structure and diversity of the cecal microbiota of broiler chickens (BC) and laying hens (LH). The 16S rRNA sequencing analysis showed Firmicutes, Bacteroidetes, and Proteobacteria were the main cecal bacterial phyla in BC and LH. However, at the genus level, LH had a greater abundance of Bacteroides (P < 0.05), Rikenellaceae_RC9_gut_group (P < 0.01), Phascolarctobacterium (P < 0.05), Desulfovibrio (P < 0.05), Prevotellaceae_UCG-001 (P < 0.05), and unclassified_o_Bacteroidales (P < 0.05), whereas BC had a greater abundance of Alistipes (P < 0.05), Rikenella (P < 0.05), Ruminococcaceae_UCG-005 (P < 0.05), Lachnoclostridium (P < 0.05), and unclassified_f_Ruminococcaceae (P < 0.05). It is particularly noteworthy that the genus Desulfovibrio was significantly more abundant in the LH cecum than in the BC cecum (P < 0.05). A metagenomic analysis showed that the annotations in the LH dataset were significantly more abundant than in the BC dataset, and included replication, recombination and repair, energy production and transformation, cell wall/membrane/envelope biogenesis, and amino acid transport and metabolism-related functions (P < 0.05). This study indicates that microbial genotypic differences in chickens of the same species can cause changes in the abundances of the gut microbiota, but do not alter the structural composition or major functional characteristics of the gut microbiota.