Objective: To verify the effect of fiducial marker number and configuration on target registration error (TRE) for dynamic computer-aided zygomatic implant surgery. Material and Methods: All patients who underwent zygomatic implant surgery with navigation from January 2018 to December 2021 were enrolled. For each patient, 6 to 8 miniscrews were placed intraorally as fiducial markers before the surgery. After the registration procedure, the TRE, which represents the distance between the target of the image space and the real position of the fiducial markers, was calculated. SPSS (22.0) was used for statistical analysis. Results: A total of 325 titanium miniscrews were placed in 47 patients who underwent zygomatic implant placement by navigation. The lowest TRE was 0.2 mm, compared to the highest TRE of 1.9 mm. There was no significant difference in the mean TRE value among the different titanium miniscrew groups ( P = .07). A total of 8 miniscrews in 7 patients were lost in the maxillary tuberosity area prior to and during navigation surgery, which resulted in an irregular polygonal distribution of fiducial markers. However, there was no statistically significant difference in TRE between a polygonal distribution (0.62 ± 0.35 mm) and an irregular polygonal distribution (0.68 ± 0.33 mm) ( P = .35). Conclusion: A scattered, polygonal distribution with of a minimum of five fiducial markers in an edentulous maxilla could achieve acceptable TRE values in registration. It seems that the registration error was not influenced by the absence of one corner in a polygon distribution.