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Restoration programs require long-term monitoring and assessment of vegetation growth and productivity. Remote sensing technology is considered to be one of the most powerful technologies for assessing vegetation. However, several limitations have been observed with regard to the use of satellite imagery, especially in drylands, due to the special structure of desert plants. Therefore, this study was conducted in Kuwait’s Al Abdali protected area, which is dominated by a Rhanterium epapposum community. This work aimed to determine whether Unmanned Aerial Vehicle (UAV) multispectral imagery could eliminate the challenges associated with satellite imagery by examining the vegetation indices and classification methods for very high multispectral resolution imagery using UAVs. The results showed that the transformed difference vegetation index (TDVI) performed better with arid shrubs and grasses than did the normalized difference vegetation index (NDVI). It was found that the NDVI underestimated the vegetation coverage, especially in locations with high vegetation coverage. It was also found that Support Vector Machine (SVM) and Maximum Likelihood (ML) classifiers demonstrated a higher accuracy, with a significant overall accuracy of 93% and a kappa coefficient of 0.89. Therefore, we concluded that SVM and ML are the best classifiers for assessing desert vegetation and the use of UAVs with multispectral sensors can eliminate some of the major limitations associated with satellite imagery, particularly when dealing with tiny plants such as native desert vegetation. We also believe that these methods are suitable for the purpose of assessing vegetation coverage to support revegetation and restoration programs.