Recently, three-dimensional (3D) facial scanning has been gaining popularity in personalized dentistry. Integration of the digital dental model into the 3D facial image allows for a treatment plan to be made in accordance with the patients’ individual needs. The aim of this study was to evaluate the effects of extraoral markers on the accuracy of digital dentofacial integrations. Facial models were generated using smartphone and stereophotogrammetry. Dental models were generated with and without extraoral markers and were registered to the facial models by matching the teeth or markers (n = 10 in each condition; total = 40). Accuracy of the image integration was measured in terms of general 3D position, occlusal plane, and dental midline deviations. The Mann–Whitney U test and two-way analysis of variance were used to compare results among face-scanning systems and matching methods (α = 0.05). As result, the accuracy of dentofacial registration was significantly affected by the use of artificial markers and different face-scanning systems (p < 0.001). The deviations were smallest in stereophotogrammetry with the marker-based matching and highest in smartphone face scans with the tooth-based matching. In comparison between the two face-scanning systems, the stereophotogrammetry generally produced smaller discrepancies than smartphones.