A comparative morphometric analysis of otoliths was done to understand the major morphometric characters responsible for differentiating two species of Green-eyes (Chlorophthalmus corniger and C. acutifrons) which is one of the dominant fish groups caught in the deep-sea trawling during the exploratory surveys as well as in the by-catch of trawlers targeting deep-sea shrimps at a depth range of 300 – 500 m in the Indian waters. A total of 53 intact, right otoliths (25 and 28 for C. corniger and C. acutifrons, respectively) were considered for the morphometric analysis to differentiate species collected from Andaman Sea. The study extracted four otolith morphometric measurements and five shape indices measured from the otoliths using image analysing software including otolith weight. The otolith morphometric parameters and shape indices showed significant relationship with the fish size were scaled with standard length to remove the influence of fish size from the data. Principal component analysis using scaled otolith morphometric measurements indicated that the first two axes described 84.78 % and 11.80 % of variation, respectively. The PC1 differentiated the species based on ellipticity and otolith weight followed by area and perimeter. C. acutifrons is differentiated from their congener with a more elliptic, heavy otolith with more otolith surface area. One-way PERMANOVA confirmed significant difference in otolith morphology between the species. Present study confirmed the suitability of otolith morphometric analysis in differentiating Chlorophthalmus species which are quite inevitable for taxonomic studies as well as for the better understanding of the species resolution in diet studies.