Validation comparisons between satellite-based surface energy balance models and tower-based flux measurements over heterogeneous landscapes can be strongly influenced by the spatial resolution of the remote sensing inputs. In this paper, a two-source energy balance model developed to use thermal and visible /near-infrared remotely sensed data is applied to Landsat imagery collected during the 2004 Soil Moisture Experiment (SMEX04) conducted in southern Arizona. Using a two dimensional flux-footprint algorithm, modeled surface fluxes are compared to tower measurements at three locations in the SMEX04 study area: two upland sites, and one riparian site. The effect of pixel resolution on evaluating the performance of the land surface model and interpreting spatial variations of land surface fluxes over these heterogeneous areas is evaluated. Three Landsat scenes were examined, one representing the dry season and the other two representing the relatively wet monsoon season. The model was run at three resolution scales: namely the Landsat visible/near-infrared band resolution (30 m), the Landsat 5 thermal band resolution (120 m), and 960 m, which is nominally the MODIS thermal resolution at near-nadir. Comparisons between modeled and measured fluxes at the three tower sites showed good agreement at the 30 m and 120 m resolutions — pixel scales at which the source area influencing the tower measurement (∼ 100 m) is reasonably resolved. At 960 m, the agreement is relatively poor, especially for the latent heat flux, due to sub-pixel heterogeneity in land surface conditions at scales exceeding the tower footprint. Therefore in this particular landscape, thermal data at 1-km resolution are not useful in assessing the intrinsic accuracy of the land-surface model in comparison with tower fluxes. Furthermore, important spatial patterns in the landscape are lost at this resolution. Currently, there are no definite plans supporting high resolution thermal data with regular global coverage below ∼ 700 m after Landsat 5 and ASTER fail. This will be a serious problem for the application and validation of thermal-based land-surface models over heterogeneous landscapes.