Zinc finger protein 132 (ZNF132) is a transcriptional repressor and plays an important role in animal production traits. Insertion/deletion (indel) polymorphisms are relatively simple and effective DNA markers. The objective of this study was to explore the potential novel indel variants within the goat ZNF132 gene, as well as to evaluate their effects on growth traits. A novel 16-bp indel was first verified in a 5′ untranslated region (UTR) of the ZNF132 gene, and three genotypes were detected. The minor allelic frequencies were 0.160 and zero in the Hainan black goat (HNBG) and Guanzhong dairy goat (GZ) breeds, respectively. Additionally, there were significant differences in the distribution of genotypic and allelic frequencies between these two breeds (P< 0.01). An association analysis revealed that the 16-bp novel indel was significantly associated with the body length of the HNBG breed (P=0.046), and that the individuals with genotype II exhibited the shortest body length, suggesting that the 16-bp indel significantly affected growth traits. These findings could extend the spectrum of genetic variations of the ZNF132 gene and provide a valuable theoretical basis via indel markers for marker-assisted selection (MAS) in goat breeding and genetics.