The well-known “factor endowment hypothesis (FEH)” implies that countries with higher scarcity in land and/or water intend to import more land-intensive and/or water-intensive goods. To more effectively test this important hypothesis, we first adopted recently available scarcity indices of land and water in the literature to distinguish scarce land and water from neutral or abundant land and water. We then incorporated land and water scarcity into multi-regional input-output analysis to quantify virtual land and water flows embodied in food trade among 140 countries/regions in 2011. The results show that while the major net exporters of virtual scarce-land are land-abundant countries, which supports the FEH, the major net exporters of virtual scarce-water were water-scarce countries, which does not support the FEH. This finding suggests that the current market forces reflect the scarcity of land resources, but does not reflect the water scarcity in the context of international trade. The reasons sustaining this distinction was discussed.