Auchenionchus crinitus and Auchenionchus microcirrhis share their distributional area along the Chilean coast. These labrisomid blennies are difficult to recognize based on the attributes described in taxonomic keys, which consist of overlapped or non-informative morphological and meristic characteristics of body parts. Sagittae otolith shape is useful for species determination; thus, the aim of our study was to evaluate the discriminant power of sagittae otoliths through analyses of shape indices and geometric morphometrics, and to describe the sagittae otolith shape of the two fish species. Four linear measurements (length, width, area and perimeter) of sagittae otoliths were considered to calculate the shape indices. Inter-specific differences were assessed by Mann-Whitney U tests for each index, and no significant differences between species were found (U = 181.5–256; p > 0.05). Based on these results, the shape indices evaluated here must not be employed for species of the genus Auchenionchus. A total of 72 landmarks contouring sagittae otoliths were considered for the geometric morphometric analysis, where the least-squares Procrustes method was followed to obtain a consensus coordinate matrix. The sagittae otolith was morphologically distinctive for each species, A. crinitus shows a wide and curved rostrum compared with A. microcirrhis, where this feature is more angled and elongated. Similarly, the posterior edge in the otolith of A. crinitus is wide in curvature, while this portion is angled in curvature in A. microcirrhis. The vertex between rostrum and anti-rostrum forms a cordiform shape in the sagittae otolith of both species, although in A. crinitus this characteristic is more prominent. A Principal Component Analysis and a Discriminant Function Analysis using the consensus coordinate matrix allowed us to confirm the differences between species according to sagittae otolith shape. Our study constitutes the first assessment of sagittae otolith shape via geometric morphometrics in the family Labrisomidae.