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Background Random flap is one kind of the most widely used skin flaps in reconstructive surgery; however, partial necrosis of its distal end remains a significant problem now. The aim of this study was to evaluate the effect of hypoxia preconditioned bone marrow mesenchymal stem cells (HpBMSCs) transplantation on ultra-long random skin flap survival in rats.Methods Normoxic bone marrow mesenchymal stem cells (nBMSCs) were cultured under normoxia (20% O2) and HpBMSCs under hypoxia (1% O2) for 48 hours before transplantation. Thirty Sprague-Dawley rats were randomly divided into control group, nBMSCs group and HpBMSCs group with each consisting of 10 rats. Survival area of ultra-long random skin flap on the dorsal of rats was measured seven days after flap surgery and cell transplantation. Cell survival in vivo, microvessel density and vascular endothelial growth factor (VEGF) were evaluated by histological examination and enzyme-linked immunosorbent assay.Results Compared with other two groups, flap survival area in HpBMSCs group was significantly larger (P ＜0.05).Microvessel density in HpBMSCs group (36.20+8.19) was higher than that in nBMSCs group (30.01±5.68) and control group (17.60±4.19) (P ＜0.05). VEGF in HpBMSCs group ((300.05±50.41) pg/g) was higher than those in nBMSCs group ((240.55±33.64) pg/g) and control group ((191.65±32.58) pg/g) (P ＜0.05).Conclusion HpBMSCs transplantation improves ultra-long random skin flap survival via promoting angiogenesis of more survival cells.