KiSS-1 gene encodes a protein product kisspeptin which are intense inducers of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) secretion in various mammalian species through its receptor GPR54 (G protein-coupled receptor-54). A total of 100 goat compromising of Red Sokoto (n = 72) and Sahel (n = 28) breeds were used to detect single nucleotide polymorphisms (SNPs) in the intronic region of the KiSS-1 gene by sequencing and investigate their relationship with other goat breeds. Nucleotide sequence analysis revealed five novel SNPs (g.1745G>A present in Red Sokoto, g.1776G>A, g.1827A>G, g.1857T>C and g.2208T>C present in Red Sokoto and Sahel breeds). To obtain a correct phylogenetic relationship between goat breeds, nucleotide sequences were compared to other sequences in NCBI database using a BLASTn algorithm and retrieved for further analysis. Neighbour-joining phylogenetic relationship tree constructed revealed two distinct clusters with ancestral lineage of 100% identity. Nigerian goat breeds (Red Sokoto and Sahel) clustered into a clade with Indian goat breeds (Ganjam and Osmanabadi) while the second cluster involved eight other goat breeds. Genetic distance estimate revealed high genetic similarity between Red Sokoto and Sahel breeds as observed in their genetic distance value of 0.003. The nucleotide sequences of the two Nigerian goat breeds (Red Sokoto and Sahel) for KiSS-1 gene were submitted to GenBank database and have accession numbers: MN122316 and MN122317, respectively. The analysis of polymorphism in KiSS-1 gene indicates that genetic variation exists in the goat breeds studied. Therefore, attempts can be made to investigate the association of these polymorphism with reproductive traits in Nigerian goat breeds.