Computed tomography (CT) scans of 212 museum specimens, including mostly cartilaginous and bony fishes as well as several reptiles and amphibians, were obtained to quantitatively study vertebral column morphology and regionalisation. The specimens are housed in the University of Cambridge Museum of Zoology or the Natural History Museum in London (specimen identification numbers can be found in the supporting documentation). These data consist of 1) series of tiff images that can be imported into CT segmenting software to reconstruct their shape in three dimensions; 2) STL files of each vertebra for a subset of the specimens scanned; 3) 3D landmark coordinates or measurements for each vertebra for a subset of taxa scanned; 4) tables of results from regionalisation analyses, and 5) photographs of eight fossil fish specimens Supplemental files include details of the data collection procedures, specimen identification numbers and updated taxonomy, and CT scanning parameters for all scans. Full details about this nonGeographicDataset can be found at https://doi.org/10.5285/1c76e443-da02-4bc4-a041-0f79adc016be