This paper presents a novel marker encoded fringe projection profilometry (FPP) scheme for efficient 3-dimensional (3D) model acquisition. Traditional FPP schemes can introduce large errors to the reconstructed 3D model when the target object has an abruptly changing height profile. For the proposed scheme, markers are encoded in the projected fringe pattern to resolve the ambiguities in the fringe images due to that problem. Using the analytic complex wavelet transform, the marker cue information can be extracted from the fringe image, and is used to restore the order of the fringes. A series of simulations and experiments have been carried out to verify the proposed scheme. They show that the proposed method can greatly improve the accuracy over the traditional FPP schemes when reconstructing the 3D model of objects with abruptly changing height profile. Since the scheme works directly in our recently proposed complex wavelet FPP framework, it enjoys the same properties that it can be used in real time applications for color objects.