The blind Mexican cavefish, Astyanax mexicanus, is a natural model for regressive evolutionary changes, such as complete eye loss, following cave colonization. An extant surface-dwelling form of this species enables powerful comparisons across complex traits. Cavefish also harbor cranial abnormalities, including fragmentation of intact bones into multiple elements. Fragmentation, first observed over 70 years ago, demonstrates radical asymmetry across the lateral axis of the face. To understand the developmental basis of bone fragmentation, we performed an intra-individual in vivo staining and visualization procedure. We compared normal growth of the third suborbital (SO3) bone in surface fish (n=16) with aberrant growth in cavefish (n=30) from the first appearance of ossification through mature bone development. Surface fish SO3 bones form from a single condensation of mesenchymal cells (“primary ossification center”) directly inferior to the eye that expanded uniformly in an antero-posterior direction. Conversely, cavefish demonstrated primary and multiple secondary ossification centers, arising spontaneously throughout development. Some ectopic ossification centers resulted in distinct fragments, while others were absorbed by the larger SO3 element. Further, the number of ossification centers differed between left and right sides of the face in juvenile cavefish, reflecting the morphological asymmetry present in adults. In sum, surface fish display typical patterns of SO3 bone growth, while aberrant and asymmetrical ossification processes underlie fragmentation in cavefish. This work reveals dynamic changes to the cranial complex in cavefish, over life history, which arose in response to the extreme pressures of the cave environment.