Vascular endothelial growth factor receptor (VEGF) plays a critical role in blood vessel formation and affects nerve growth and survival. VEGF receptor 2 (Flk1) functions as the major signal transducer of angiogenesis, mediating VEGF induction of endothelial tubulogenesis. We have cloned and analyzed expression of Flk1 in the blind subterranean mole rat Spalax ehrenbergi. Spalax experience abrupt and sharp changes in oxygen supply in their sealed underground niche and, hence, are genetically adapted to hypoxia and serve as a unique, natural mammalian model organism for hypoxia tolerance. Spalax Flk1 is relatively conserved at the nucleic acid and amino acid level compared to human, mouse, and rat orthologs. Reverse transcription-quantitative polymerase chain reaction was used to analyze Flk1 expression in muscle and brain of animals exposed to ambient or variant hypoxic oxygen levels at multiple stages of development. Transcript levels were compared with those obtained from Rattus, a primary model for human physiology. Our findings demonstrate that under normoxic conditions Flk1 patterns of expression correlate well with our previous investigations of VEGF expression. Exposure to hypoxic conditions resulted in divergent patterns of Flk1 expression between Spalax and Rattus and between muscle and brain. It appears that the regulatory mechanisms differentiating expression between the species and between tissues are most likely unique, suggesting that Flk1 expression may be regulated by multiple processes, including both angiogenesis and neurogenesis.—Band, M., Shams, I., Joel, A., Avivi, A. Cloning and in vivo expression of vascular endothelial growth factor receptor 2 (Flk1) in the naturally hypoxia-tolerant subterranean mole rat.