The high prolific Zaraibi and low prolific Barki are among Egypt's most common indigenous goat breeds. The prolificacy of goat herds can be increased by selecting animals having single-nucleotide polymorphisms (SNPs) in fecundity-related genes. Herein, we detailed the use of DNA sequences followed by quantitative polymerase chain reaction (qPCR) and high-resolution melting curve (HRM) analysis to detect SNPs in exon 2 of the prolificacy-linked gene GDF9 and investigate their association with prolificacy in Zaraibi (n = 100) and Barki (n = 100) goats. The results of DNA sequencing (n = 20/breed) were used as a reference for genotyping the remaining DNA samples using qPCR-HRM. A non-synonymous SNP p.V371M/c.1111G>A in was detected in GDF9 of Zaraibi goats, however, Barki goats were monomorphic for this locus. The three genotypes of the c.1111G>A SNPs were significantly associated with litter size in Zaraibi goats. Homozygous mutant genotypes (c.1111AA) had significantly higher litter sizes than other genotypes (P < 0.05). Based on these findings, we recommend selecting Zaraibi goats with c.1111AA genotypes to increase the prolificacy of this breed.