The reproduction efficiency of rams has a strong impact on flock productivity, and the fertility of a flock is very diverse even when it is exposed to similar environmental and management conditions. There is no clear information on how these differences are caused by biological factors, especially in the heat stress seasons such as summer. There is also emerging evidence that the seminal microbiome can have an effect on the reproductive performance of the male, although the interactions between the seminal microbiome and hormonal profiles and testicular characteristics in rams has not been well established. It is important to clarify this critical gap in order to identify reliable fertility biomarkers and enhance the choice of superior breeding males. Of note, this experiment investigated the relationships among seminal microbiome composition, testicular morphometry, and reproductive parameters in rams during summer. A total of 386 ewes and 9 rams were used in an entirely randomized study, and rams were categorized and grouped based on the level of superior, good, and acceptable fertility according to the rate of pregnancy. The microbiome was characterised through 16S rRNA gene sequencing. Clostridiaceae was positively associated with fertility status, and the relative abundance of Clostridiaceae was 98.38%, 87.03%, and 59.57% in superior, good, and acceptable fertility categories, respectively. Superior-fertility rams had a higher concentration of testosterone (3343.75 pg/ml) than acceptable-fertility rams did (1242.72 pg/ml, P < 0.0001). Specific bacterial signatures were found to be fertility-specific, with some families specific to certain fertility groups. The results form a basis for establishing microbiome-based strategies for enhancing ram reproductive performance.