Immunophilins were discovered as cellular receptors for immunosuppressive drugs: cyclosporine A and FK506. Cyclophilins (CYPs, receptors for cyclosporine A) and FK506-binding proteins (FKBPs, receptors for FK506) do not share sequence homology, but have a common feature of peptidyl-prolyl cis-trans isomerase (PPIase) activity that catalyzes the cis-trans conversion of X-Pro peptide bonds, a rate-limiting step in the process of protein folding. Immunophilins are widely present in organisms from bacteria and fungi, to animals and plants. Genomics studies revealed that plants possess the largest immunophilin family. However, the physiological function of plant immunophilins is poorly understood. In this review, starting with a brief introduction of the immunophilin family and the current knowledge about their physiological roles in diverse organisms, the recent advances in the elucidation of plant immunophilin's physiological roles, largely via functional genomics tools, are summarized here. Notably, a striking feature of plant immunophilins is that a large fraction is localized in the chloroplast. Recent studies reveal that chloroplast immunophilins play a central role in the assembly and maintenance of photosynthetic complexes.