Automated marker detection allows real time image guidance for treatment setup in 6D and intra-beam monitoring in 3D on a standard linear accelerator. This study retrospectively assessed the accuracy and efficiency of automated marker registration vs. manual match from a group of treated prostate SBRT patients.An automated marker detection scheme was developed by reconstructing a 3D marker model from orthogonal paired images for pre-treatment setup alignment using iterative closest point (ICP). The 3D marker model was back-projected to monoscopic x-ray images acquired during treatment. 3D marker motion was estimated from the consecutive (40o gantry angle apart) monoscopic x-ray images. Standard treatment was 2 arc Volumetric-modulated arc therapy (VMAT) plan prescribed to 8 Gy per fraction (x5). From 9 SBRT prostate patients, 135 paired images and 810 monoscopic x-ray images were analyzed using the automated scheme by comparing to the 3D marker model of planning image. A subgroup of the data set (5 patients, 12 fractions, 235 monoscopic images) were re-aligned to 3D marker position of setup images from the automated program to compare marker motion without realignment, which had minor residual setup error after manual match. Paired sample Wilcoxon ranked test was run to evaluate the improvement of using automated alignment, P-value < 0.05 was considered significant.Using automated marker match as reference, the residual setup error after manual match of the entire group (135 paired images) was (0.3 ± 0.6) mm, (0.1 ± 0.7) mm, (0.2 ± 0.8) mm in lateral (Lat), longitudinal (Long), vertical (Vert) directions, and (-2.6 ± 5.0)o, (-0.1 ± 2.8)o, (-1.3 ± 3.0)o in pitch, yaw, roll directions, respectively. The centroid of the marker position had an error of (0.2 ± 1.2) mm, (-0.6 ± 1.3) mm, (0.7 ± 1.4) mm in Lat, Long, Vert directions, respectively, during treatment (from 810 images). Treatment error at Lat, Long, Vert directions had stronger correlation with setup error in Lat & roll (-0.57 & -0.18), in Long & yaw (-0.49 & -0.25), and in Vert & roll (0.48 & 0.31), respectively. The magnitude of the improvement for individual fraction of the subgroup (235 images) using automated setup correction was 0.4 mm, 0.4 mm, 0.4 mm in Lat (P < 0.01), Long (P = 0.04), Vert (P = 0.39). The fraction of the treatment time that the marker centroid had a positional error of more than 2mm (a tolerance which triggered treatment interruption) was 9.5%, 18.5%, 12% in Lat, Long, Vert directions, respectively, using manual setup match, and 2.5%, 8.5%, 0.5% using automated setup match.This study demonstrated the ability of automated marker match to improve the accuracy and efficiency of prostate SBRT during treatment using monoscopic x-ray image. The improvement of treatment accuracy was 0.4 mm in each (X, Y, and Z) dimension. The improvement treatment efficiency was 50% reduction of treatment interruption which needs re-imaging. In addition, auto-registration saves manual markers alignment time.