The otoliths of teleost fishes exhibit a great deal of inter-and intra-species shape variation. The ecomorphology of the saccular otolith is often studied by comparing its shape across species and populations inhabiting a range of environments. However, formal tests are often lacking to examine how closely variation in otolith shape follows the genetic drift of a neutral trait. Here, we examine patterns of saccular otolith shape variation in four species of African cichlid fishes, each sampled from three field sites. All four species showed the greatest level of otolith shape variation along two principal component axes, one pertaining to otolith height and another to the prominence of an anterior notch. fish collected from the same site possessed similarities in saccular otolith shape relative to fish from other sites, and these 'site-difference' signatures were consistent across species and observable in both sexes. Sex-differences in saccular otolith shape differed in magnitude from site to site. Population differences in saccular otolith shape did not covary with neutral genetic differentiation between those populations. Otolith height, in particular, displayed large site similarities across species, weak correlation with neutral genetic variation, and strong sex differences, collectively suggesting that otolith shape represents a selectively non-neutral trait. The otoliths of the inner ears of teleost fishes represent a powerful lens for studying many aspects of fish biology including their ecology, neurobiology, bioacoustics, systematics, and fisheries stock assessments 1-3. The morphology of teleost otoliths, i.e. their size and shape, is of particular interest, especially with respect to the saccular otolith. This is because the saccular otolith often displays high levels of morphological differentiation between species, and also notable differentiation within species, making it an important tool for fish biologists 4. Saccular otolith shape alone can aid in discriminating between fish species (e.g. Serranus spp. 5 ; rockfish spp. 6), and also between stocks/populations, sexes, age-classes, and reproductive morphs (e.g. Atlantic cod, Gadus morhua 7 ; plainfin midshipman fish, Porichthys notatus 8 ; flatfish spp. 9 ; round goby, Neogobius melanostomus 10). Yet, the processes that give rise to such specific otolith shapes remain largely unknown, and represent a major outstanding evolutionary question about the structure and function of teleost otoliths 3. Intraspecific shape variation in saccular otoliths can be affected by a multitude of factors, including developmental, genetic, and environmental factors. While the saccular otoliths of young fish are often relatively simple in form, they frequently take on more complex, species-specific shapes as the fish grow 4,11. Otolith shape is also, in part, genetically determined, as exemplified by Vignon and Morat 12 , who showed that coral reef snapper, Lutjanus kasmira, that live and grow under the same environmental conditions can have differently shaped saccul...