Objectives <p>The Wanxi White Goose (<i>Anser cygnoides</i>) is a large waterfowl of the Anatidae family and one of the most prominent medium-sized goose breeds in China. This breed has been observed to exhibit several distinctive characteristics, including accelerated early growth, robust stress resistance, substantial egg-laying performance, and elevated down production. The egg-laying performance of Wanxi White Geese is influenced by genetic factors, as well as by environmental and feeding management factors. In this study, the intestinal contents from the high-laying and low-laying Wanxi white geese were collected, and the 16 S amplicon sequencing method was used to evaluate the relationship between the composition of intestinal bacterial communities and their egg-laying ability.</p> Data description <p>The 16 S rDNA sequencing technology was utilized to sequence and identify the microorganisms present in the duodenum, jejunum, ileum, and cecum of Wanxi white geese with varying egg-laying abilities. Four biological replicates were collected from each sample across all sections, resulting in a total of 32 samples for subsequent sequencing studies. All raw DNA sequences were uploaded to the Genome Sequence Archive (GSA) database of the National Genomics Data Center (NGDC), which is under the China National Center for Bioinformation. The accession number assigned to the submission is CRA028174, and the BioProject number is PRJCA043467. The clean read sequencing lengths for most samples ranged from 200 to 450 bp.</p> Clinical trial number <p>Not applicable.</p>