Abstract Fish are the most diverse vertebrate group, and they have evolved equally diverse visual systems, varying in terms of eye morphology, number and distribution of spectrally distinct photoreceptor types, visual opsin genes and opsin gene expression levels. This variation is mainly due to adaptations driven by two factors: differences in the light environments and behavioural tasks. However, while the effects of large‐scale habitat differences are well described, it is less clear whether visual systems also adapt to differences in environmental light at the microhabitat level. To address this, we assessed the relationship between microhabitat use and visual system features in fishes inhabiting coral reefs, where habitat partitioning is particularly common. We suggest that differences in microhabitat use by cardinalfishes (Apogonidae) drive morphological and molecular adaptations in their visual systems. To test this, we investigated diurnal microhabitat use in 17 cardinalfish species and assessed whether this correlated with differences in visual opsin gene expression and eye morphology. We found that cardinalfishes display six types of microhabitat partitioning behaviours during the day, ranging from specialists found exclusively in the water column to species that are always hidden inside the reef matrix. Species predominantly found in exposed microhabitats had higher expression of the short‐wavelength‐sensitive violet opsin ( SWS2B ) and lower expression of the dim‐light active rod opsin ( RH1 ). Species of intermediate exposure, on the other hand, expressed opsins that are mostly sensitive to the blue‐green central part of the light spectrum ( SWS2A s and RH2 s), while fishes entirely hidden in the reef substrate had a higher expression of the long‐wavelength‐sensitive red opsin. We also found that eye size relative to body size differed between cardinalfish species, and relative eye size decreased with an increase in habitat exposure. Retinal topography did not show co‐adaptation with microhabitat use, but data suggested co‐adaptation with feeding mode. We suggest that, although most cardinalfishes are nocturnal foragers, their visual systems—and possibly those of other (reef) fishes—have also adapted to the light intensity and the light spectrum of their preferred diurnal microhabitats. A free Plain Language Summary can be found within the Supporting Information of this article.