A method and system for automatic landmark registration and registration using trajectory information and shape sensing during an endoscopic procedure, such as bronchoscopy, are described herein. A segmentation centerline of airways of a lung may be generated based on a pre-operative computed tomography (CT) image of the lung. Landmarks may be automatically detected on the segmentation centerline corresponding to bifurcations in the airways of the lung. A location data point cloud of locations of a catheter through the airways of the lung during navigation may be generated. A bounding volume of the airways of the lung may be generated and a bounding volume centerline may be detected. Landmarks may be detected on the bounding volume centerline for the same bifurcations. Then, the two sets of landmarks may be mapped as part of registration. The trajectory information with shape sensing may be used to provide non-rigid or fine registration.