The authors report on the micron scale characterization of a monolithic GaN microcavity (MC) with lattice matched AlInN/GaN distributed Bragg reflectors by means of a microtransmission setup. This technique allows extracting very high quality factors (Q up to 2800), in accordance with theoretical predictions, contrary to what was previously reported for nitride based MCs. Furthermore, two-dimensional mappings of the MC transmission spectrum allow probing the disorder in this MC. The direct relationship between an increased disorder and a reduction in the Q factor is clearly observed. (c) 2006 American Institute of Physics.