Wild canid populations exhibit different anatomical morphologies compared to domesticated dogs in North America. This is particularly important concerning archaeological sites, which may contain early domesticated species, for the proper identification of osteological remains. Previous studies have indicated domestic dogs exhibit a shorter rostrum accompanied by a crowded tooth row; however, none describe the overall complexity of these changes. Consequently, using a landmark‐based geometric morphometric analysis, cranial morphological characteristics were examined in North American wild canids: the gray wolf (Canis lupus), coyote (Canis latrans), red wolf (Canis rufus), and the domestic dog (Canis familiaris). The shape and size of the cranium in lateral and ventral views were compared between the three wild species to the group of domesticated dogs. Wild canids clustered separately from the domestic group in all statistical analyses. Results indicate an expansion of the orbital region, a compression of the rostrum, and an overall warping in the shape and orientation of the skull. In domestic species, there is also a downward shift in the frontal portion of the skull accompanied by the braincase assuming a more upward position. This technique successfully depicted how slight changes in isolated areas of the cranium can have an impact on the overall shape and morphology of the skull. We presume these changes in cranial anatomy reflect the recent selective pressures domestic dogs have undergone since diverging from their wild ancestors. Copyright © 2012 John Wiley & Sons, Ltd.