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The anatomical and morphometric (shape indices, contour descriptors and otolith weight) characterizations of sagittal otoliths were investigated in 13 species of Lutjanus spp. inhabiting the Persian Gulf. This is the first study that compares the efficiency of three different image analysis techniques for discriminating species based on the shape of the outer otolith contour, including elliptical Fourier descriptors (EFD), fast Fourier transform (FFT) and wavelet transform (WT). Sagittal otoliths of snappers are morphologically similar with some small specific variations. The use of otolith contour based on wavelets (WT) provided the best results in comparison with the two other methods based on Fourier descriptors, but only the combination of the all three methods (EFD, FFT and WT) was useful to obtain a robust classification of species. The species prediction improved when otolith weight was included. In relation to the shape indices, only the aspect ratio provided a clear grouping of species. Also, another study was carried on to test the possibility of application of shape analysis and comparing otolith contour of otoliths of Lutjanus johnii from Persian Gulf and Oman Sea to identify potential stocks. The results showed the otoliths have differences in contour shape and can be contribute to two different stocks.