We report the development and analysis of a velocimetry technique based on the short time displacement of molecular tracers, tagged thanks to photobleaching. We use confocal microscopy to achieve a good resolution transverse to the observation field in the direction of the velocity gradient. The intensity profiles are fitted by an approximate analytical model which accounts for hydrodynamic dispersion, and allow access to the local velocity. The method is validated using pressure driven flow in microfluidic slits having a thickness of a few tens of micrometers. We discuss the main drawbacks of this technique which is an overestimation of the velocity close to the walls due to the combination of molecular diffusion and shear. We demonstrate that this error, limited to a near wall region of a few micrometers thick, could be controlled by limiting the diffusion of fluorophore molecules or minimizing the bleaching time. The presented technique could be combined with standard particle imaging velocimetry to access velocity differences and allow particle trajectory analysis in microflows of suspensions.