Osteocytes play a central role in bone metabolism in extant vertebrates, but their evolutionary history is poorly understood. Therefore osteocyte lacunae microstructure of fossil bone was studied on the nanometer scale by means of focused ion beam tomography (FIB). A osteostracan and a “placoderm” were imaged, the earliest groups with cellular bone, and secondary osteons respectively. To visualize and characterize the early bone composition via the morphology and distribution of osteocyte lacunae, thereby imaging the predecessor to all modern bone cells. The data provided represents two fossil samples (with 2 files each): Bothriolepis trautscholdi. (Antiarchi, 'Placodermi'), MB.f.9188 (Late Devonian, ~372-382 million years ago). The sample was measured using a ZEISS Crossbeam 340 with an original voxel size of 30 nm. The "9188_Bothriolepis_normlized_bin2_60nm.zip" file represents the two times binned and normalized image stack. "MB.f.9188.mesh_files.zip" represents the derived surface information. Tremataspis mammillata. (Osteostraci), MB.f.9025 (Late Silurian; ~423-428 million years ago). The sample was measured using a ZEISS Crossbeam 340 with an original voxel size of 20 nm. The "9025_Tremataspis_normalized_nocrack_bin2_40nm.zip" file represents the two times binned and normalized image stack. Additionally a crack in the measured volume has been removed. "MB.f.9025.mesh_files.zip" represents the derived surface information. The surface information data contains the .blend, .obj, .x3d and the .stl file format. The volume data consists of .tif images.