Otolith morphometrics has been shown to provide a practical basis for stock discrimination and ageing. This approach has been extensively used by fisheries scientists over the last decades. However, the determinants of otolith shape are not fully understood and shape apparently results from the synergistic action of various confounding factors. In this study, I used a geometric morphometric approach to quantitatively investigate the concomitant effect of local environmental conditions and ontogeny on otolith shape. I specifically focused on the ontogenetic trajectories of otolith shape in a coral reef fish (Lutjanus kasmira) during an ontogenetic shift in habitat use, from juveniles settled in the estuary to adults inhabiting either the channel or the outer-reef off French Polynesia. Data emphasize that both ontogeny and environmental conditions influence otolith shape in an interactive way, potentially mediated by growth rate. More specifically, during the early life stages living in the estuary, otolith shape is mainly linked to fish size, indicating an ontogenetically determined development that induces an overall reshaping of the otoliths. In contrast, the transition from the estuarine to the reef life is considered as a crucial phase in fish life history, as revealed by an important change in the ontogenetic rate and direction of the otolith development for both habitats. After the shift in habitat use, otolith demonstrated divergent ontogenetic growth patterns, not in terms of heterochrony but in the magnitude and direction of morphological changes. This indicates that growth axis can be completely reshaped by environmental conditions, with respect to allometric component. This information is fundamental if otolith shape is to be used in fisheries management as an effective tool for modeling age-structured populations and stocks as a function of the use made of the habitat during life span.