This dataset comprises Fastq files of sequencing data used in the study "Characterization of microbiota communities of ewe’s vaginal tract and its potential impact on reproductive efficiency," developed by the same team. The data includes RNA 16s raw sequencing reads generated from the vaginal microbiota of ewes. Metadata associated with each sample are also included. These data were analyzed to investigate the composition and diversity of microbial communities and their potential influence on reproductive performance.