This dataset contains the raw confocal laser scanning microscopy (CLSM) slices and X-ray microtomography (micro-CT) slices for the holotype of Paraodontomma leptocristatum (NIGP174676) from mid-Cretaceous Burmese amber. Additional confocal data for Paraodontomma szwedoi (NIGP169926) are also provided. This dataset is associated with the publication "New species of Paraodontomma from mid-Cretaceous Burmese amber with muscle tissue preservation (Coleoptera: Archostemata: Ommatidae)" (DOI:10.11606/1807-0205/2021.61.53). Confocal images were obtained with a Zeiss LSM710 confocal laser scanning microscope, using 488 nm Argon laser excitation line. Both original CZI files and exported TIFF stacks are provided. Micro-CT data were obtained with a Zeiss Xradia 520 Versa 3D X-ray microscope. Scanning parameters were as follows: isotropic voxel size, 9.4355 μm; power, 4 W; acceleration voltage, 50 kV; exposure time, 1.5 s; projections, 2201. The TIFF stack is provided.