The variation in the kidding size of Black Bengal and Sirohi breed of goats makes them an interesting genetic material to study the underlying genetic mechanism of prolificacy. Accordingly, we studied the comparative ovarian morphometry including disparity in numbers of antral follicles of different sizes between these two breeds. Further, we evaluated the differential expression of the important candidate genes (viz., BMP15, GDF9 and BMPR1B) known to influence the ovulation rates and the prolificacy. The ovaries of Black Bengal (n = 20) goat were lighter (p < 0.01) in weight and smaller (p < 0.01) in diameter than those of Sirohi (n = 19) goats but possessed more numbers (p < 0.05) of corpus luteum (CL), large and small antral follicles. Quantitative real-time PCR (RT-qPCR) analysis revealed differential expression of mRNAs encoding for the BMP15 and GDF9. Small antral follicles of Black Bengal goats expressed 2.78-fold more (p < 0.05) of BMP 15 than those of Sirohi goat. Expression of BMP15 (p < 0.01) and GDF9 (p < 0.05) mRNAs was more abundant in the small than the large antral follicles of Black Bengal goat. The more numbers of antral follicles per unit of ovarian mass and differential expression of BMP15 and GDF9 may serve as an important clue for higher prolificacy.