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Accurate quality information on cloud occurrence is of utmost importance for a wide range of remote-sensing applications and analyses. This study compares the two existing cloud mask products available for the Moderate Resolution Imaging Spectroradiometer (MODIS), stored in the quality layer of the MOD09 daily surface reflectance product. For both masks, statistics on cloud occurrence are calculated for 1 year of daily surface reflectance data covering the area of southeast Asia. Furthermore, a cloud mask enhancement algorithm is presented for increasing cloud flag reliability by effectively combining the existing cloud labels together with the utilization of annual statistics based on the blue reflectance band. Furthermore, since a lot of compositing algorithms rely on cloud mask information for the filtering of unsuitable observations, the influence of the different cloud masks on 8-day MOD09A1 composite outputs is examined with respect to data availability and average view angles. The results of the statistical analysis show that the accuracy of the two cloud mask products differs significantly for southeast Asia. Particularly, the radiative influence of land cover proves to strongly affect the reliability of the cloud flags, although to varying degrees throughout the year. The enhancement algorithm successfully identifies undetected clear observations in the original masks while simultaneously setting upper limits for atmospheric contamination. In this manner, considerably higher proportions of cloud-free observations can be retained compared to a clear-sky conservative combination of the masks as applied in other compositing algorithms.