Cyclophilins (CYPs) are a group of ubiquitous proteins characterized by their ability to bind to the immunosuppressive drug cyclosporin A. The CYP family occurs in a wide range of organisms and contains a conserved peptidyl-prolyl cis/trans isomerase domain. In addition to fulfilling a basic role in protein folding, CYPs may also play diverse important roles, e.g. in protein degradation, mRNA processing, development, and stress responses. We performed a genome-wide database survey and identified a total of 94 CYP genes encoding 91 distinct proteins. Sequence alignment analysis of the putative BnCYP cyclophilin-like domains revealed highly conserved motifs. By using RNA-Seq, we could verify the presence of 77 BnCYP genes under control conditions. To identify phloem-specific BnCYP proteins in a complementary approach, we used LC-MS/MS to determine protein abundances in leaf and phloem extracts. We detected 26 BnCYPs in total with 12 being unique to phloem sap. Our analysis provides the basis for future studies concentrating on the functional characterization of individual members of this gene family in a plant of dual importance: as a crop and a model system for polyploidization and long-distance signalling.As one of the most important crops for nutritional oil, fodder, biodiesel, chemical and pharmaceutical products, Brassica napus (oilseed rape or canola) is widespread in agriculture, especially in the European Union, China, and Canada. Beside its essential agricultural significance, B. napus has also become a model plant for studying long-distance signalling 1-5 and evolutionary consequences of polyploidization 6,7 . Brassica napus is used as a model plant for studying long-distance signalling, because methods for the collection of sufficient quantities of pure xylem and phloem sap are well established 2, 4 . Compared to crops like wheat, soybean or rice, the domestication of B. napus was more recent. It is assumed that chromosome doubling occurred after spontaneous hybridization between Brassica rapa (Asian cabbage or turnip rape, 2n = 2 × 10 = 20, genome AA) and Brassica oleracea (Mediterranean cabbage, 2n = 2 × 9 = 18, genome CC) 8 . The profitable cultivation of B. napus (genome AACC, 2n = 38) has high importance for the economy 9 .A group of proteins involved in diverse fundamental cellular functions in many different organisms is called immunophilins, originally discovered as receptors for immunosuppressive drugs in mammals. The family of immunophilins consists of two major groups, FK506-binding proteins (FKBPs) 10, 11 and cyclophilins (CYPs) 12,13 . Despite the lack of sequence and structure similarity, FKBPs and CYPs each possess a conserved domain responsible for their common peptidyl-prolyl cis/trans isomerase (PPIase) activity, catalyzing the rate-limiting rotation of X-proline peptide bonds from a cis to a trans conformation 14 . These domains are called the FKBP and cyclophilin-like domain (CLD), respectively. An additional group of proteins exhibiting PPIase activity, the parvulins, cannot be clas...