In the sand-dune region across the Israel–Egypt border, an anomalous phenomenon of thermal variation was observed on remote sensing images: the Israeli side with much more vegetation cover has higher surface temperature than the Egyptian side, where bare sand surface prevails. The study intends to examine the phenomenon using NOAA-AVHRR and Landsat TM data. The focus is to analyse the seasonal and spatial change of land surface temperature (LST) in the border region, to verify it through ground truth measurements and to simulate the average LST change on both sides according to surface composition structure. A split window algorithm containing only two parameters (transmittance and emissivity) has been developed for retrieving LST from NOAA-AVHRR data and a mono-window algorithm is proposed for computing LST from the only one thermal band of Landsat TM data. Application of these algorithms to the available AVHRR and Landsat TM data indicates that the LST anomaly does occur not only in one day but almost all the year. In hot dry summer the Israeli side is usually about 2.5–3.5°C hotter. In wet cool winter the LST difference between the sides is not large but the Israeli side still has higher LST. The Egyptian side may have slightly higher LST when surface temperature is below 20°C, several days after heavy rain, which leads to very wet surface conditions. The sharp LST contrast disappears on night-time images. Ground truth measurements indicate that the LST contrast mainly can be attributed to the surface temperature difference on the two typical surface patterns: biogenic crust and bare sand, which have above 3°C difference in surface temperature during summer. Experiments on soil samples from the field indicate that biogenic crust and sand have emissivity values of about 0.972 and 0.954, respectively, in hot dry conditions that match the environment of the region in summer. Surface composition determination based on three methods indicates that more than 72% of the ground on the Israeli side is covered with biogenic crust and more than 80% on the Egyptian side is bare sand. Actually, the LST anomaly can be understood as the direct result of surface composition difference, especially in biogenic crust and sand cover rate. Simulation with this surface composition difference shows that the Israeli side has steadily higher LST when the temperature of the biogenic crust is more than 1°C higher that of the sand surface, which usually occurs at moderate to high temperature levels (>30°C). When temperature is between 15 and 25°C, such as at about midnight, the two sides will have no obvious LST difference. This result is in agreement with the remote sensing observation. Therefore, it can be concluded that the vegetation cover does not contribute much to the LST contrast in comparison to the effect of the biogenic crust and sand cover.