Vertebrate animals localize sounds by comparing differences in the acoustic signal between the two ears and, accordingly, ear structures such as the otoliths of fishes are expected to develop symmetrically. Sound recently emerged as a leading candidate cue for reef fish larvae navigating from open waters back to the reef. Clearly, the integrity of the auditory organ has a direct bearing on what and how fish larvae hear. Yet, the link between otolith symmetry and effective navigation has never been investigated in fishes. We tested whether otolith asymmetry influenced the ability of returning larvae to detect and successfully recruit to favourable reef habitats. Our results suggest that larvae with asymmetrical otoliths not only encountered greater difficulties in detecting suitable settlement habitats, but may also suffer significantly higher rates of mortality. Further, we found that otolith asymmetries arising early in the embryonic stage were not corrected by any compensational growth mechanism during the larval stage. Because these errors persist and phenotypic selection penalizes asymmetrical individuals, asymmetry is likely to play an important role in shaping wild fish populations.