BackgroundThe inhibin alpha (INHA) gene is one of the important genes affecting the reproductive traits of animals. Hainan black goats are the main goat breed in Hainan Island (China), whose development is limited by low reproductive performance. However, the relationship betweenINHAgene and the reproductive performance of Hainan black goats is still unclear. Therefore, the purpose of this work was to explore the effect ofINHAgene polymorphisms on the litter size of Hainan black goats.MethodsSingle nucleotide polymorphisms (SNPs) ofINHAwere detected, and the genetic parameters and haplotype frequency of these SNPs were calculated and association analysis was performed for these SNPs with the litter size. Finally, the SNP with significant correlations to litter size was analyzed by Bioinformatics tools.ResultsThe results showed that the litter size of individuals with theACgenotype at loci g.28317663A>C ofINHAgene was significantly higher than those with theAAgenotype. This SNP changed the amino acid sequence, which may affect the function ofINHAprotein by affecting its structure. Our results suggest that g.28317663A>C loci may serve as a potential molecular marker for improving the reproductive traits in Hainan black goats.