Background: Understanding differences in tissue morphology has not been well researched, yet provides crucial insight into evolution. We investigate the effect of eye reduction on the shape of surrounding bones by examining two morphs of the Mexican tetra (Tinaja cavefish and sighted fish), F1 intermediates, zebrafish, a sighted tetra after lens removal and a zebrafish mutant, bum-/-, which has a degenerating lens. Results: Significantly, by comparing the skulls, we show that there are broadly similar effects on bone shape after eye reduction with bones posterior and dorsal to the eye consistently most affected in both species. We conclude that there are conserved mechanisms underlying bone shape changes in response to a reduced or lost eye. Of interest, when we compare the shapes of individual bones and the mode of eye reduction, differences suggest that the finer details of these underlying mechanisms may indeed vary. We also show that cavefish occupy a unique morphospace with respect to skull morphology and that F1 intermediates are most similar to sighted fish than their cavefish parent. Conclusions: This study highlights the dynamic nature of the vertebrate skull and its ability to respond to tissue changes within the head, a topic which has been largely overlooked in the literature. Developmental Dynamics 244:1109-1120, 2015. [copyright] 2015 Wiley Periodicals, Inc.