To identify co-accelerated evolution regions(accelerated regions for short) of Bos taurus and Capra hircus at whole genome-wide, and reveal the potential molecular mechanism under the evolution of the unique phenotype of bovids, we performed homologous genomic regions of 14 species the whole genome sequencing and bioinformatics analysis of genes with accelerated evolution events in coding regions, the enriched GO term, KEGG pathways and histone modification regions. The results showed that a total of 44 794 accelerated regions were detected in genome of Bos taurus and Capra hircus. These acceleration regions were distributed in both the gene region and the non-gene region, accounting for 54.80 % and 45.20 % of the total, respectively. In addition, accelerated regions were significantly enriched in 25 active sites of histone. A total of 2703 candidate genes occurred accelerated evolution events in coding regions. Gene Ontology analysis indicated that these candidate genes were mainly involved in biological processes like axon genesis, gland development, muscle tissue development, cellular components like synaptic membrane, axon membrane, axon part, post-synaptic density. KEGG pathways showed that these candidate genes were mainly involved in cAMP signaling pathways, axon guidance signaling pathways, calcium signaling pathway and Neuroactive Ligand-Receptor Interaction. It indicated that during the formation of the horn in bovids, unique changes occur in the production of synapses and axons, which affects signal transmission and leads to the changes in transcription regulation and gene expression, resulting to the appearance of morphologically specific horns in bovids.