Anchovy (Engraulis ringens) population units were analyzed in three zones off the coast of Chile: 1: Arica-Iquique, 2: Coquimbo and 3: Talcahuano-Valdivia from samples obtaineds during the 2012 spawning season. We used 50 left sagittae otoliths from each zone to perform a morphometric analysis, which included basic measurements, shape indexes and contour analysis (elliptical Fourier analysis). A MANOVA and Tukey multiple comparison analyses, applied on basic measures and shape indexes showed significant differences between zone 3 and zones 1 and 2. A classification by Canonical Discriminant analysis of elliptical Fourier harmonics, indicated significant differences among zones. It is concluded, therefore, that otolith shape analysis could be used to discriminate population units of Engraulis ringens. Better results were achieved using elliptic Fourier coefficients than using only shape indices.