Bembrops caudimacula dominates the deep-sea trawl catch in the exploratory surveys and as bycatch in the commercial trawling targeting deep-sea shrimps, in the Indian Exclusive Economic Zone. The intra-species variability in the bathy-demersal fish Bembrops caudimacula collected from two different ecosystems in the Indian Ocean were studied using otolith morphometric analysis. Five otolith size parameters (ferret length, ferret width, area, perimeter and weight), and five shape indices (roundness, rectangularity, ellipticity, form factor and circularity) were taken from forty-seven otoliths collected from two regions. Principal component analysis (PCA) and non-parametric PERMANOVA successfully differentiate the fishes from two regions based on the otolith morphometry. PCA indicated that ellipticity and otolith weight were the major factor responsible for the variation. The study indicated that otoliths of the fishes collected from Andaman Sea (part of Bay of Bengal) were more elliptic and massy compared to those collected from the Arabian Sea. This is the first work on the differentiation of