Jebel Marra, a volcanic complex in western Sudan, is an important site of early settled agriculture, with high plant diversity, supported by orographic rainfall. Vegetation types were examined in relation to habitat, altitude, soils, and land management. In 52 sites, 274 species, predominantly Fabaceae and Poaceae, were recorded (with 17 new records). Sites were clustered using TWINSPAN, and Detrended Correspondence Analysis (DCA), generating eight vegetation types, six new since the 1970s. Changes in the dominant species show that the savanna has become sparser, with annuals displacing perennials. Soils were mostly “sandy clay loams,” so vegetation types did not directly correspond to soil types, although Type VIII vegetation grew in soils with a higher clay content. The sand fraction that predominated in soils of all other vegetation types was, mainly (87%) “soft” or aeolian sand. Canonical Correspondence Analysis (CCA) separated communities and species along a first axis, associated with finer soil textures, higher Fe, and lower elevations. The second axis was positively associated with elevated phosphorus, and negatively with sandy loams. CCA showed that rainfall alone was less pertinent than soil texture, which determines plant-available water capacity. The region’s vegetation was not uniformly diverse; instead, a mosaic of patches of diverse terrain, associated with different vegetation “types,” collectively generates a diverse flora. Besides climate change, overgrazing and increasing human pressures due to conflict, local population growth and an influx of refugees place these (already stressed) plant resources at risk. Our survey provides a baseline to track changes and develop adaptive management strategies.