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An appropriate combination of rice cultivar and cropping system that maximizes water use efficiency (WUE) may improve yield of rainfed lowland rice. In the paddy field, a large amount of water is consumed by evaporation during the early growth period, and it can be reduced by canopy coverage especially in semi-arid regions. Therefore, we evaluated the role of canopy coverage in WUE of rice in the early growth period in semi-arid region. A pot experiment was conducted in Namibia to investigate the genotypic and species difference in WUE, and another pot and a field experiment were conducted to investigate the effects of planting density on WUE. Although no significant difference was observed among species, the mean WUE was in the decreasing order of Oryza sativa, and Oryza glaberrima followed by the interspecific progenies including NERICA. In contrast, there was a significant difference in WUE at the genotypic level. Highly tillering genotypes such as WAB1159-2-12-11-5-1 and WITA 2 showed a high WUE. Furthermore, WUE was significantly correlated with the number of tillers (R-2 = 0.453), and higher planting density resulted in a higher WUE. In contrast, stomatal conductance had no significant correlation with WUE (R-2 = 0.081). Thus, the physical conditions affected by number of tillers and planting density had greater impacts on WUE than physiological characteristics such as stomatal conductance. The suppression of surface water evaporation by coverage was significant, probably contributing to WUE improvement. To increase WUE in semi-arid regions, we recommend the increase of canopy coverage and higher planting density.