Genetic diversity of three Indian goat breeds namely Barbari, Sirohi and Black Bengal goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymorphism in two candidate genes (GDF9 and BMP4) in a sample of 90 goats with 30 goats of each breed. Both of the studied loci were polymorphic, having three variants for GDF9 and two variants for BMP4, in the studied population. Polymorphic information content (PIC) criterion revealed an intermediate polymorphism for all analysed phenotypic groups for Barbari, Sirohi and Black Bengal goats. Effective allele number criterion also revealed equally diverse nature of these genes. This preliminary study provides insight into the genetic diversity of Barbari, Sirohi and Black Bengal goats at GDF9 and BMP4 gene locus, which can be utilized for further study polymorphism and association of these polymorphic variants with traits of economic traits in future.