Natural killer (NK) cells are a diverse population of lymphocytes with a range of biological roles including essential immune functions. NK cell diversity is created by the differential expression of cell surface receptors which modulate activation and function, including multiple subfamilies of C-type lectin receptors encoded within the NK gene complex (NKC). Little is known about the gene content of the NKC beyond rodent and primate lineages, other than it appears to be extremely variable between mammalian groups. We compared the NKC structure between mammalian species using new high quality draft genome assemblies for cattle and goat, re-annotated sheep, pig and horse genome assemblies and the published human, rat and mouse lemur NKC. The major NKC genes are largely in syntenic positions in all eight species, with significant independent expansions and deletions between species, allowing us to present a model for NKC evolution during mammalian radiation. The ruminant species, cattle and goats, have independently evolved a second KLRC locus flanked by KLRA and KLRJ and a novel KLRH-like gene has acquired an activating tail. This novel gene has duplicated several times within cattle, while other activating receptor genes have been selectively disrupted. Targeted genome enrichment in cattle identified varying levels of allelic polymorphism between these NKC genes concentrated in the predicted extracellular ligand binding domains. This novel recombination and allelic polymorphism is consistent with NKC evolution under balancing selection, suggesting this diversity influences individual immune responses and may impact on differential outcomes of pathogen infection and vaccination.