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Focusing on the central Kalahari, this study utilized fractional cover of photosynthetic vegetation (f(PV)), non-photosynthetic vegetation (f(NPV)) and bare soil (f(BS)), derived in situ and estimated from GeoEye-1 imagery using Multiple End-member Spectral Mixture Analysis (MESMA) and object-based image analysis (OBIA) to determine superior method for fractional cover estimation and the impact of vegetation morphology on the estimation accuracy. MESMA mapped fractional cover by testing endmember models of varying complexity. Based on OBIA, image was segmented at five segmentation scales followed by classification. MESMA provided more accurate fractional cover estimates than OBIA. The increasing segmentation scale in OBIA resulted in a consistent increase in error. Different vegetation morphology types showed varied responses to the changing segmentation scale, reflecting their unique ecology and physiognomy. While areas under woody cover produced lower error even at coarse segmentation scales, those with herbaceous cover provided low error only at the fine segmentation scale.