This study presents a comprehensive bibliometric analysis of literature on the microbiome of reproductive systems in farm animals, utilizing data from the Web of Science (WoS) and Scopus databases. The primary aim was to evaluate the scientific content and bibliometric characteristics of articles published on the reproductive tract microbiome in farm animals. The advanced tool Bibliometrix was employed to explore bibliometric networks, providing insights into the scope of microbiome research within this field. Findings indicate that research in reproductive microbiomes is still emerging, with significant contributions from developed countries, particularly the United States, China, Brazil, and Spain. The field remains heavily focused on bovine studies, while substantial knowledge gaps persist regarding other livestock, including ovines, caprines, and camelids. One of the most notable advancements in this area has been the adoption of next-generation sequencing (NGS), which has shifted microbiome research away from labour-intensive, culture-based methods to culture-independent, high-throughput approaches. Although NGS has significantly facilitated the study of bacterial communities within reproductive systems, limited research has been conducted on fungal and viral microbiomes. This bacterial emphasis is partly due to the accessibility and cost of NGS technologies, which remain prohibitively high for many institutions in developing regions, thus limiting participation. Clustering analysis identified three main themes: genetic influences on pregnancy, microbial-reproductive health interactions, and male fertility with a focus on sperm quality. Additionally, emerging research topics were identified, including microbial species associated with reproductive diseases in livestock.