In this paper we analyze the characteristics of an experimental otolith identification system based on image contours described with Elliptical Fourier Descriptors (EFD). Otoliths are found in the inner ear of fishes. They are formed by calcium carbonate crystals and organic materials of proteic origin. Fish otolith shape analysis can be used for sex, age, population and species identification studies, and can provide necessary and relevant information for ecological studies. The system we propose has been tested for the identification of three different species, Engraulis encrasicholus, Pomadasys incisus belonging to the different families (Engroulidae and Haemolidae), and two populations of the species Merluccius merluccius (from CAT and GAL) from the family Merlucciidae. The identification of species from different families could be carried out quite easily with some simple class identifiers -i.e based on Support Vector Machine (SVM) with linear Kernel-; however, to identify these two populations that are characterized by a high similarity in their global form; a more accurate, and detailed shape representation of the otoliths are required, and at the same time the Otolith identifiers have to deal with a bigger number of descriptors. That is the principal reason that makes a challenging task both the design and the training of an otolith identification system, with a good performance on both cases.