Otoliths are very useful biomarkers especially for fish growth. Climate change with the associated global changes in warming and acidification could affect the calcification and the shape of otoliths during the crucial larval period in teleost fish. To evaluate this predicted combined effect of temperature and CO2, Atlantic herring (Clupea harengus) embryos and larvae were reared from hatching to respectively 47 and 60 days post-hatching (dph), under present day conditions and a scenario predicted for the year 2100 (IPCC RCP8.5). Otolith morphogenesis was tracked by analyzing area and normalized Elliptical Fourier coefficients. We found that otolith area for fish of similar size increased under the predicted 2100 climate change scenario compared to the present day. Climate change does not, however, seem to directly affect the otolith shape. Finally, the onset of otolith morphogenesis is hardwired, but the relationship between otolith and fish size is environment-dependent.