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Simple Summary: The Sox gene family is a set of specific transcriptional factor (TF) proteins, with a very similar sequence compared to the sex-determining region Y (SRY), related high-mobility group (HMG) box genes found in mammals. The Sox gene family is involved in many important developmental processes, including sex determination. In the current study, an in silico analysis was performed to provide insights into the evolutionary importance, mutations and gene duplication events of the buffalo Sox gene family. Based on our analysis, we found that the HMG domain was highly conserved throughout the Sox gene family. Mutational analysis revealed twenty non-synonymous mutations with potential detrimental effects on physiological functions in buffalo. The current study concluded that the buffalo Sox gene family was highly conserved throughout evolution, and the non-synonymous mutations identified could potentially be valuable for the selective breeding of buffalo. The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo. [ABSTRACT FROM AUTHOR]