Otolith-shape analysis was examined to determine its utility for biological stock identification of the bogue Boops boops along the Algerian coast of the Mediterranean Sea. The outlines of 179 sagittal otolith pairs from fish collected at three locations (Oran, Bejaia and Annaba) between 2013 and 2016 were digitised and analysed for shape variation by elliptical Fourier analysis. Potential confounding sources of variation (fish length, age and sex, and left or right otolith position) were examined and accounted for in the analyses before interpretation of spatial differences in distribution of the stock. Redundancy analysis showed a significant difference between the left and right otoliths. No difference was correlated with sex and age, but fish length and sampling location had a significant effect on otolith shape. Differences in otolith shape between fish from the three locations (a span of approximately 1 000 km) were not large enough to support the concept of separate biological stocks of B. boops along the Algerian coast, as illustrated by the scatterplot of discriminant scores. This study emphasises the need to carefully evaluate the confounding effects of the otolith side (left or right) on the Fourier descriptors of otoliths before drawing conclusions about stock structure of the bogue on the basis of otolith-shape differences among samples of fish from different stocks or areas.