Human needs on protein, especially those kinds protein derived from animal, are increasing day by day along with the increasing of human population on earth. Various aspect on livestock production requires more attention from the farmer. Nowadays due to advance biotechnology many genetically control aspects of livestock can be improved based on interest. Previous researches investigated that Beta-defensin have an important function on animal host defense system. However, there is limited study on Beta-defensin gene especially in goat, and the role of Single Nucleotide Polymorphism (SNP) as a factor corelated to genetic diseases or phenotypic traits in animal. Thus, on this bases that we carried out this research.Twelve (12) Chinese goat breeds were used on a series of gene amplification. SNP confirmation test was done and a single nucleotide mutation was found from T to C, between 1349-1363 bp (exon 2) within the goat’s Beta-defensin sequence of the population used. Population genetics analysis for each breed revealed that C allele as mutant allele common with samples from Sichuan province. This allele occurred more frequent in three of six Sichuan populations. F-statistic analysis on each breed resulted to negative FIS value per population ranging from -0.029 in BR population to -1.000 in LZ population, and there were only 2 populations having positive FIS value 0.202 and 0.235 NJ and CM population respectively. Nm value resulted from this research was 2.0022. Gene diversity value (He) ranged from 0.510 highest in JT population to 0.054 lowest in BR population. All of this condition might likely be caused by inbreeding and or small size of the researched population.An in-depth research needs to be done to investigate the effect of inbreeding, native blood deterioration, and to find which factors are responsible for disequilibrium within the said population.