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This study was designed to examine the subtle effects of habitat, aspect and altitude on plant diversity and the timing of phenological stages. In this increasingly arid region, within-species differences would cause more reproductive isolation of local populations, making species more vulnerable to regional extinction. Fifty-two sites in the Jebel Marra region of the Central Darfur state of Sudan were compared in terms of species diversity and local variation in the phenology of plant communities. Five habitat types were compared: sandy plains, clay plains, wadis, north-facing slopes and south-facing slopes. Sites were classified into five altitudinal zones ranging from 750 m to > 1,150 m above sea level, and the phenology of three categories of plant life form (phanerophytes, chamaephytes and therophytes) was tracked in terms of the duration of each phenophase (vegetative, reproductive and dormant). Overall, most plants were dormant from December to April. Peak vegetative growth was in July, coinciding with peak rainfall in all study sites in the region (July-August). This was followed by peak reproduction in October. Life form and habitat type significantly affected the length of all phenological phases; altitude significantly affected all stages except the duration of dormancy. Some of the interactions between these factors were also statistically significant, indicating subtle regulation of the duration of phenophases. The possible impacts of overgrazing and ongoing climate change are discussed, with the concern that initiation of vegetative growth in most habitats (except the clay plains) appears to be triggered by day length, anticipating’ the beginning of the rainy season. Further climate change may uncouple this signal and the beginning of the rainy season, impacting plant survival.