This study focused on the analysis of semi-arid natural vegetation phenology in the Northern Negev in Israel during the two growing seasons in 2010/2011 and 2012/2013 with different precipitation patterns. The objective was to develop a methodology based on vegetation indices to detect the characteristic phenological cycles of three types of vegetation, annual grasses, perennial shrubs and biological soil crusts, with multi-temporal RapidEye data. For the first time the usage of RapidEye's high temporal resolution as well as its red edge band enabled a detailed detection of this phenology in semi-arid environments. In doing so, the vegetation indices differed in their suitability for the different vegetation types. One could benefit from the Normalized Difference Vegetation Index (NDVI) for annual plants, the Normalized Difference Red Edge Index (NDRE) for perennial plants and the Modified Normalized Difference Vegetation Index (MNDVI) for biological soil crusts. The spatial distribution of the vegetation is illustrated by combining the three indices during their maximal photosynthetic activity.