Simple SummaryThis study will assist in the conservation of genetic resources and breeding planning for the sustainable utilization of Thai swamp buffalo. It is essential to clearly understand the diversity of genetic resources for breeding planning and genetic conservation. High genetic variation has the potential to exist, and vice versa; the species may easily become extinct when low genetic variation exists. The study revealed that the indicators of the genetic diversity of the swamp buffalo population were also genetically diverse in theTLR2coding region, as assessed by nucleotide diversity, and that genetic diversity was high. This indicates that it is easy to select and improve the available genetic tools to improve health and production in swamp buffalo when the populations are diverse. The authors suggest thatTLR2gene variations may have the potential for marker-based breeding programs aimed at breeding better disease resistance in swamp buffalo.AbstractToll-like receptors (TLRs) are transmembrane proteins important for directing immune responses. Their primary role is to recognize pathogens based on single-nucleotide polymorphism (SNP) characteristics. TLR2 is categorized as a pattern recognition receptor (PRR) that is important for the recognition of pathogens. Nucleotide variation in the coding region determines the conformation of the TLR protein, affecting its protein domain efficiency. This study aimed to identify SNPs in the coding region ofTLR2to enhance available genetic tools for improving health and production in swamp buffalo. A total of 50 buffaloes were randomly sampled from the northeastern part of Thailand for genomic DNA extraction and sequencing. Nucleotide sequences were aligned and compared with cattle and river buffalo based on the database. The results showed, there were 29 SNP locations in swamp buffalo and 14 different locations in both cattle and buffaloes. Haplotype analysis revealed that 27 haplotypes occurred. Swamp buffalo were identified from 13 SNPs based on biallelic analysis, which found eight synonymous and five nonsynonymous SNPs. Nucleotide diversity (π) was 0.16, indicating genetic diversity. Genetic diversity (haplotype diversity; HD) was high at 0.99 ± 0.04. This indicates a high probability that the two sample haplotypes are different. The π and HD values are important indicators of the genetic diversity of the swamp buffalo population. In summary, the Thai swamp buffalo population detected a polymorphism of the coding region of theTRL2gene. Therefore, further, in-depth study of the relationship between these genes in the immune system and disease resistance should be recommended.