In the field of forensic odontology, not only personal identification using oral conditions, including dental treatment marks and DNA typing, but also species identification, age or sex estimation using cranial or partial bones, and time after death may also be applicable as estimation methods. Among these many tasks, one of the most difficult is species identification of fragmented calvarium. This is because the calvarium has poor morphological features, except that it is a flat bone, and few reports have described how to differentiate it. In this study, a simple identification method for turtle shell (carapace and plastron) whose morphological characteristics closely resembled those of the calvarium was applied. As a result, in an enlarged image obtained using a stereoscopic microscope, the characteristics of each suture pattern could be confirmed. In the decalcified and non-decalcified bone specimens, the difference in the inner/outer laminar structure and the specific structural difference of the cancellous bone-equivalent part were confirmed. Furthermore, most of the features could be obtained in the destructive inspection when it was examined using micro CT imaging to determine whether discrimination by nondestructive inspection was possible or not. No significant difference in ingredients was found using the Electron Probe X-ray Micro Analyzer. The calvarium was more calcified than the carapace but less calcified than the plastron. From these results, we suggest that micro CT imaging is effective for discriminating between the calvarium and turtle shell in a short time.