The objective of the current study was to detect the incidence of FecX G mutation in 141bp fragment of exon 2 of BMP-15 gene in Beetal goat and to determine its phylogenetic relationship with other goat breeds. In this study 60 Beetal goats were randomly selected and divided equally into two groups on the basis of their body weights. The PCR-RFLP and DNA sequencing techniques were employed to explore polymorphism in exon 2 of BMP-15 gene. Upon digestion with Hinf1, the purified product showed heterozygous carriers with two bands (111bp, and 54bp) in all animals. The analysis of polymorphism for FecX G in Beetal goat indicates that the genetic factor responsible for difference in growth rates is not related to the reported mutated alleles of BMP-15 gene. Therefore, it is suggested that polymorphisms in the other regions of BMP-15 gene should be explored which might be responsible for the difference of growth rates in Beetal goat. Phylogenetic tree of mRNA of BMP-15 gene was constructed and the results revealed Teddy as outgroup. Moreover, among all the breeds used in this analysis Teddy is also phenotypically different from other due to its smaller size and greater prolificacy. However, all the remaining breeds were present in a single large clade, with Black Bengal and Markhoz goat in a further single sub-clade and showing maximum divergence from the common ancestor. The Beetal was next to Black Bengal and Markhoz and along with their common ancestor they were present in a single clade.