Objectives In humans, there is a large range of variation in the form of the maxillary and mandibular dental arches. This variation can manifest as either prognathism or retrognathism in either or both arches, which can cause malocclusion and lead to abnormal masticatory function. This study aims to identify aspects of variation and morphological integration existing in the dental arches of individuals with different types of malocclusion. Methods Coordinate landmark data were collected along the gingival margins of 397 scanned dental casts and then analyzed using geometric morphometric techniques to explore arch form variation and patterns of morphological integration within each malocclusion type. Results Significant differences were identified between Class II forms (increased projection of upper arch relative to the lower arch) and Class III forms (lower arch projection beyond the upper arch) in symmetrical shape variation, including anteroposterior arch discrepancies and abnormal anterior arch divergence or convergence. Partial least squares analysis demonstrated that Class III dental arches have higher levels of covariance between upper and lower arches (RV = 0.91) compared to the dental arches of Class II (RV = 0.78) and Class I (RV = 0.73). These high levels of covariance, however, are on the lower end of the overall range of possible masticatory blocks, indicating weaker than expected levels of integration. Conclusions This study provides evidence for patterns of variation in dental arch shape found in individuals with Class II and Class III malocclusions. Moreover, differences in integration found between malocclusion types have ramifications for how such conditions should be studied and treated. Am. J. Hum. Biol. 28:879–889, 2016. © 2016Wiley Periodicals, Inc.