Recent advances in imaging technologies, such as intra‐oral surface scanning, have rapidly generated large datasets of high‐resolution three‐dimensional (3D) sample reconstructions. These datasets contain a wealth of phenotypic information that can provide an understanding of morphological variation and evolution. The geometric morphometric method (GMM) with landmarks and the development of sliding and surface semilandmark techniques has greatly enhanced the quantification of shape. This study aimed to determine whether there are significant differences in 3D palatal rugae shape between siblings. Digital casts representing 25 pairs of full siblings from each group, male–male (MM), female–female (FF), and female–male (FM), were digitized and transferred to a GM system. The palatal rugae were determined, quantified, and visualized using GMM computational tools with MorphoJ software (University of Manchester). Principal component analysis (PCA) and canonical variates analysis (CVA) were employed to analyze palatal rugae shape variability and distinguish between sibling groups based on shape. Additionally, regression analysis examined the potential impact of shape on palatal rugae. The study revealed that the palatal rugae shape covered the first nine of the PCA by 71.3%. In addition, the size of the palatal rugae has a negligible impact on its shape. Whilst palatal rugae are known for their individuality, it is noteworthy that three palatal rugae (right first, right second, and left third) can differentiate sibling groups, which may be attributed to genetics. Therefore, it is suggested that palatal rugae morphology can serve as forensic identification for siblings.