Understanding, monitoring, and managing savanna ecosystems requires characterizing both functional and structural properties of vegetation. From a functional perspective, in savannas, quantitative estimation of fractional cover of photosynthetic vegetation (fPV), non-photosynthetic vegetation (fNPV), and bare soil (fBS) is important as it relates to carbon dynamics and ecosystem function. On the other hand, vegetation morphology classes describe the structural properties of the ecosystem. Due to high functional diversity and structural heterogeneity in savannas, accurately characterizing both these properties using remote sensing is methodologically challenging. While mapping both fractional cover and vegetation morphology classes are important research themes within savanna remote sensing, very few studies have considered systematic investigation of their spatial association across different spatial resolutions. Focusing on the semi-arid savanna ecosystem in the Central Kalahari, this study utilized fPV, fNPV, and fBS derived in situ and estimated from spectral unmixing of high- (GeoEye-1), medium- (Landsat TM), and coarse- (MODIS) spatial resolution imagery to investigate: (i) the impact of reducing spatial resolution on both magnitude and accuracy of fractional cover; and (ii) how fractional-cover magnitude and accuracy are spatially associated with savanna vegetation morphology classes. Endmembers for Landsat TM and GeoEye-1 were derived from the image based on purity measures; for MODIS (MCD43A4), the challenge of finding spectral endmembers was addressed following an empirical multi-scale hierarchical approach. GeoEye-1-derived fractional estimates showed comparatively closest agreement with in situ measurements and were used to evaluate Landsat TM and MODIS. Overall results indicate that increasing pixel size caused consistent increases in variance of and error in fractional-cover estimates. Even at coarse spatial resolution, fPV was estimated with higher accuracy compared with fNPV and fBS. Assessment considering vegetation morphology of samples revealed both morphology- and cover-specific differences in accuracy. At larger pixel sizes, in areas with dominant woody vegetation, fPV was overestimated at the cost of mainly underestimating fBS; in contrast, in areas with dominant herbaceous vegetation, fNPV was overestimated with a corresponding underestimation of both fPV and fBS. These results underscore that structural and functional heterogeneity in semi-arid savanna both impact retrieval of fractional cover, suggesting that comprehensive remote sensing of savannas needs to take both structure and cover into account. © 2014 © 2014 Taylor & Francis.