Background: Macrophages arising from microglia and monocyte-derived macrophages (MDMs) have extensively studied and characterized in spinal corda injury. However, the infiltration of MDMs and the precise phenotypes of the two different populations during spinal cord ischemia and reperfusion injury (SCIRI), remains ambiguous. Methods: The SCIRI model was established by transient aortic occlusion followed by reperfusion. The Basso mouse scale (BMS) was used to quantify hind limb locomotion over the following three weeks. The histopathology of the spinal cord was evaluated by hematoxylin-eosin (HE) staining and NF-200 histochemistry. In addition, the expression of macrophage polarization phenotype were observed by double immunofluorescences, real-time PCR, and flow cytometry. Results: Compared with the Sham group, all mice in the SCIRI group developed acute paraplegia after reperfusion, gradually recovering neurological function by day 21. HE staining revealed that SCIRI induced evident pathological changes in the spinal cord. M1-type genes (iNOS, TNF-α, CD86, and CD16) were dramatically upregulated, mainly during the 1st week of SCIRI, whereas the M2 genes, CD206, and CD204, were elevated at a later stage. In addition, double-immunofluorescence confirmed in these activated microglia/macrophages phenotypes that CD86 and CD206 were co-localized. Finally, flow cytometry further demonstrated the infiltration of MDMs (CD11b+ CD45high cells) that were principally a pro-inflammatory M1 type, which peaked at day 3 and decreased by day 7 post-injury. Conversely, microglia (CD11b+CD45low cells), rather than invading MDMs, was the principal source of M2 polarized cells.Conclusions: SCIRI induced a transient influx of MDMs characterized by a M1 pro-inflammatory type, whereas resident microglia essentially maintained an M2 anti-inflammatory phenotype at later stage. These findings suggest that there is a differential regulatory role in the two cell populations following SCIRI.