The MSY of the mammalian Y-chromosome was evolved as the consequence of progressive differentiation of sex chromosomes. The complete gene content of MSY is unavailable in mammals except for human and chimpanzee. We investigated the bovine MSY and its genomic features through a deep-sequencing approach. The bovine MSY is ~ 40 Mb and contains three major regions: X-degenerate (Xd), Y-ampliconic (Ya), and Y-transitional (Yt). Xd splits into two regions (Xd1& Xd2) located at either end of MSY, spanning 2.6 Mb. Xd1 comprises nine single-copy genes (EIF1AY, OFD1Y, USP9Y, UTY, DDX3Y, ZFY, EIF2S3Y, ZRSR2Y, and RPL23AY), two (ZRSR2Y & RPL23Y) of which are bovid-specific; Xd2 harbors only two genes (SRY and RBMY). Ya was identified from two regions (Ya1 & Ya2), spanning 32.7 Mb. The majority of Ya (96%) shares intra-chromosomal similarities ≥99%, containing elaborate arrays of inverted repeats embedded with four major gene families (ZNF280BY, ZNF280AY, TSPY, and HSFY) with copy numbers ranging from ~80 to 230. ZNF280BY and ZNF280AY are bovid-specific. Each inverted repeat (~420 Kb) represents a repetitive unit, which was repeated up to ~80 times. Yt (~5 Mb) is located between Ya1 and Ya2, displaying a transitional feature between Xd and Ya, where an X-degenerate gene (UBE1Y) and a bovid-specific gene family (PRAMEY, 8 copies), are present. In addition, 93 novel single-copy transcription units (TUs) and 304 ampliconic TUs were identified from the MSY. Notably, the majority of the bovine MSY genes/TUs are expressed predominantly in testis, suggesting a role in male reproduction.