Abstract Hypoxia, which promotes tumor invasion and metastasis, is a common phenomenon in solid tumors. Hypoxia generally leads to a higher expression level of hypoxia inducible factor‐1 (HIF‐1) in tumors (cells) relative to normal tissues (cells). Given the unique expression of HIF‐1α in human cancers and its vital importance in mediating hypoxic adaptation, we have identified 20 different HIF‐1α‐specific nanobodies by using a llama‐derived nonimmune phage display library. PAS‐B domain of HIF‐1α (HIF‐1α‐PAS‐B) has been used as an antigen. Nanobody (VHH16) was selected from these 20 nanobodies by phage enzyme‐linked immunosorbent assay. The preliminary analysis of biological activity demonstrates that VHH16 can specifically bind to HIF‐1α with high affinity. VHH16 is the first nanobody that specifically binds to HIF‐1α‐PAS‐B as well. We suggest here that VHH16 is useful in disease diagnosis and also has potential in medical applications.