Otolith of mesopelagic fishes stranded in the Canary Islands during June 2021 were measured. This dataset contains the standard length (SL, mm) of each species, as well as the otolith length (OL, in mm) and width (OW, in mm), the aspect ratio (OAR = OW/OL) and the otolith relative length (ORL = (100*(OL/SL)) for each specimen. The species were identified using the external morphological identification and the otoliths analysis. We used the AFORO website for the identification of species using the otolith contour (Lombarte et al. 2006).