This study emphasized the importance to develop new molecular tools to accurately identify candidate genes in predicting semen quality in bulls that can be used in livestock production. We assessed the frequency distribution of molecular markers linked to insulin growth factor I, follicle stimulating hormone (FSH), luteinizing hormone (LH) and leptin genes in Braford and Hereford population. All bulls (Braford and Hereford; n = 188) showed good body condition scores throughout the experiment. Blood sampling and measurements of scrotal circumference were performed on weaned bulls at 7 and 24 mo of age during the bull breeding soundness evaluations. Semen collection was performed using an electroejaculator on bulls at 24, 28, 32 and 36 mo. Blood samples for DNA extraction were collected by puncture of the coccygeal vein. Five microsatellites or short tandem repeats (HEL5, AFZ1, ILSTS002, BMS3004, and IDVGA-51) and 2 SNP markers (LHR and FSHR) were evaluated by the amplification of DNA products, which then underwent electrophoresis in 10.5% polyacrylamide gel. Molecular markers were analyzed with PROC GLM ANOVA using SAS and significant were considered when < P < 0.05. Hereford bulls that expressed the variation in the IDVGA51 allele was associated (P < 0.05) with sperm motility and vigor traits in Hereford bulls. Hereford animals showed polymorphic information content (PIC) of 0.36 to 0.75% along with expected heterozygosity (H) of 0.49 to 0.78%. However, Braford bulls that expressed the ILSTS002 and AFZ1 alleles were associated (P < 0.05) with major and minor defects, respectively. Braford PIC ranged from 0.28 to 0.78% with an expected H of 0.35 to 0.81%. We found no relation between HEL5, BMS3004, LHR and FSHR to predict semen quality in bulls (P > 0.05). Therefore the present study revealed that 3 microsatellite alleles are important male reproductive biomarkers for improving semen parameters in bulls. We concluded that the ILSTS002 and AFZ1 alleles in the Braford and the IDVGA51 allele in the Hereford may be used for improving the reproductive traits in bulls.