Otolith shape analysis has been used in a number of studies as an inexpensive and powerful method for categorising fish in individual stocks. Elliptical Fourier analysis was used on three different amphidromous Sicyopterus species. Sicyopterus lagocephalus is a widespread species while the other two have a limited distribution area, Sicyopterus aiensis being endemic to Vanuatu, and Sicyopterus sarasini to New Caledonia. Both endemics live in sympatry with the widespread species. The otolith shape of all fish sampled was a clear species differentiator, thereby demonstrating that otolith shape is species-specific. At an intraspecific level there are different river populations within samples from Vanuatu, indicating a western group and an eastern "central" group.These results are congruent both for the endemic species, S. aiensis and for the cosmopolitan species. Finally, we found that, for S. lagocephalus, the cosmopolitan species, New Caledonian samples are close to western Vanuatu samples, the latter two being well differentiated from the eastern "central" Vanuatu samples. The explanation for these results may lay either in the influence of environmental factors on the otolith shape, or in the influence of common early life history thus reflecting genetic factors, or a combination of both.