We compare the quality factor values of the whispery gallery modes of microdisks incorporating GaN quantum dots (QDs) grown on AlN and AlGaN barriers by performing room temperature photoluminescence (PL) spectroscopy. The PL measurements show a large number of high Q factor (Q) resonant modes on the whole spectrum which allows us to identify the different radial mode families and to compare them with simulations. We report a considerable improvement of the Q factor which reflect the etching quality and the relatively low cavity loss by inserting QDs into the cavity. GaN/AlN QDs based microdisks show very high Q values (Q > 7000) whereas the Q factor is only up to 2000 in microdisks embedding QDs grown on AlGaN barrier layer. We attribute this difference to the lower absorption below bandgap for AlN barrier layers at the energies of our experimental investigation.