- Abstract The Israel–Egypt border region composed of longitudinal sand dunes is a very unique arid environmental ecosystem in the world: the Israeli side with much more vegetation cover has notably higher land surface temperature (LST) during daytime than the Egyptian side where bare sand prevails. In order to understand this thermal anomaly and its scientific significance in the arid environmental ecosystem development, a series of intensive research activities have been conducted in the past several years, including remote sensing analysis and meteorological modeling. In the paper, we present part of the series studies on the issue: the ground temperature measurement and emissivity determination. The region is mainly composed of four basic surface patterns: biogenic crust, bare sand, vegetation and playa (physical crust). Our hypothesis to occurrence of the thermal anomaly is that it is the direct result of the different surface composition structures and ground emissivities on both sides. Results from our ground temperature measurements during 1997–1998 validate the hypothesis of a significant LST difference existing among the main surface patterns of the region. Biogenic crust covering 72% on the Israeli side and only about 12% on the Egyptian side has an average kinetic surface temperature of above 3°C higher than bare sand. Emissivity of the two most important surface patterns also presents a significant difference. Biogenic crust has an average emissivity ranging from 0.9671 at low temperature to 0.9725 at high temperature. Bare sand occupying above 80% of the surface on the Egyptian side and only about 7% on the Israeli side has an average emissivity between 0.9435 and 0.9543. On the basis of the ground temperature measurements, we use the estimated surface cover percentage to factor the emissivity for a simple simulation of average LST on both sides, which results in an outcome that strongly support the explanation of the thermal anomaly in the border region. Since biogenic crust that covers most surface of the region plays important functions in arid ecosystem development and is common in several deserts such as north Africa and central Australia, our documentation of its surface temperature change and determination of its emissivity, which have not been seen in the literature, will provide valuable scientific basis for other studies on arid environmental ecosystems.