Bovine rumen is inhabited by diverse microbiota that plays important roles in feed digestion, nutrient uptake and energy metabolism. Rumen microbiota is essential to animal production and is affected by animal feeds and dietary additives. Dietary polyphenols can modulate the diversity and function of rumen microbes and improve animal health and productivity. Cowpea based feeds have health and production benefits for ruminants but the effect of cowpea polyphenols on bovine rumen microbiome is yet to be elucidated. The objective of this study was to evaluate the effect of cowpea polyphenols on bovine rumen microbial composition and population. Rumen fluid collected from Holstein-Friesian heifers (n = 3) was treated with cowpea phenolic extract (CPE) for 48 h. Genomic DNA was isolated from the rumen of CPE-treated and control groups and high-throughput sequencing of 16s rRNA gene on an Illumina HiSeq platform was performed. Sequence data were aligned, assembled, and analyzed using MSR: Metagenomics Version: 1.0.0, MSR Version: 2.4.60.8. CPE treatment resulted in variation in rumen microbial communities and composition (P < 0.05) at all taxonomic levels.The phyla Firmicutes (40.9%), Proteobacteria (30.5%) and Bacteroidetes (15.7%) were the dominant bacterial communities in the rumen. CPE treatment enhanced the abundance of many taxa belonging to Bacteroidetes, Firmicutes and Tenericutes phyla, while methanogenic archaea were reduced. Cellulolytic and fibrolytic bacterial communities were altered by CPE. Overall, treatment with CPE affected the rumen microbial population and diversity. In addition to the impact of cowpea on animal health and production, these results show that cowpea polyphenols modulate the rumen microbiome in cow.