Gut microbes are closely associated with disease onset and improvement. However, the effects of gut microbes on the occurrence, prevention, and treatment of benign prostatic hyperplasia (BPH) are still unclear. We investigated the alteration of gut microbiota with implications for the diagnosis, prevention, and treatment of BPH and identified correlations among various indicators, including hormone indicators, apoptosis markers in BPH, and finasteride treatment models. BPH induction altered the abundance of <i>Lactobacillus</i>, <i>Flavonifractor</i>, <i>Acetatifactor</i>, <i>Oscillibacter</i>, <i>Pseudoflavonifractor</i>, <i>Intestinimonas</i>, and <i>Butyricimonas</i> genera, which are related to BPH indicators. Among these, the altered abundance of <i>Lactobacillus</i> and <i>Acetatifactor</i> was associated with the promotion and inhibition of prostate apoptosis, respectively. Finasteride treatment altered the abundance of <i>Barnesiella</i>, <i>Acetatifactor</i>, <i>Butyricimonas</i>, <i>Desulfovibrio</i>, <i>Anaerobacterium</i>, and <i>Robinsoniella</i> genera, which are related to BPH indicators. Among these, altered abundances of <i>Desulfovibrio</i> and <i>Acetatifactor</i> were associated with the promotion and inhibition of prostate apoptosis, respectively. In addition, the abundances of <i>Lactobacillus</i> and <i>Acetatifactor</i> were normalized after finasteride treatment. In conclusion, the association between apoptosis and altered abundances of <i>Lactobacillus</i> and <i>Acetatifactor</i>, among other gut microbes, suggests their potential utility in the diagnosis, prevention, and treatment of BPH.