Follicle-stimulating hormone (FSH) plays an essential role in mammalian spermatogenesis and follicular development. In a previous study, we demonstrated that some bulls carry numerous linked mutations in the FSH beta-subunit (FSHB) gene, and that these bulls have poor-quality semen, low fertility, and slightly lower serum FSH concentration compared to those without such mutations. Here, we identified the different FSHB mRNA transcripts in such individuals and analyzed the evolutionary pattern of the FSHB open reading frame (ORF) in different species. Two different lengths of FSHB mRNA transcripts corresponding to two different polyadenylation sites in the 3'-UTR were detected in wild-type bull pituitary glands, and four different mRNA transcripts resulting from the different polyadenylation sites and linked mutations were identified in mutation-bearing bull pituitaries. All transcripts had almost the same putative FSHB precursor molecule. When the ORF sequences of wild-type and mutation-bearing genes were compared with those of other tetrapod species, the leopard frog had the lowest level of homology (57.8 and 58.1%) and the buffalo had the highest level (95.9 and 96.7%), respectively. These results indicated that the bovine FSHB gene transcribes at least two classes of mRNA in the wild-type and four classes of mRNA in the mutation-bearing individuals, which provides a new insight into the bovine FSHB evolutionary pattern. In addition, these findings lay a foundation for further study of gene expression regulation and the effects of mutations on male fertility traits in cattle.