Geometric morphometrics is a new approach for shape identification in diagnosis of malocclusion. Lateral cephalogram is an X-ray that taken for diagnosing malocclusion in dental setting. The aim of this study was to determine the differences of craniofacial shape in malocclusion by application of two-dimensional geometric morphometrics and to compile the database of malocclusion in adult Malaysian population. Lateral cephalogram radiographs of 381 adults Malaysia (age 18-45) were retrieved retrospectively and assigned to three groups according to their occlusion: class I, class II, and class III. The geometric morphometric shape study incorporated nine landmarks and was analyzed in details using tpsUtil p software. Geometric morphometric analysis such was done using MorphoJ software. The results of the principal component's analysis (PCA) yielded 14 main components responsible for 100% of the variation exhibited by the malocclusion with three highly significant PCA. The highest Mahalanobis distances were exhibited by the malocclusion class II and III population. The Procrustes ANOVA showed that the shape effect was highly significant (P<0.01). The discriminant function analysis showed the high percentage of 80% discriminate among the malocclusions after cross-validation. There are significant differences for ANB angle (A point-Nasion-B point) in all malocclusion groups. Class II has the widest ANB angle while class III has the most acute ANB angle. Skeletal shape was clearly associated with dental malocclusion and showed considerable variation. Geometric morphometrics is an alternative research tool and can be used for diagnosing individual classification of malocclusion.