We have identified nine cyclophilins encoded in the genome of the fission yeast Schizosaccharomyces pombe (Sp). Cyclophilin 3 is an orthologue of hUSA-CyP, which is associated with Prp4/Prp3 in the [U4/U6.U5] snRNP complex and Prp18, both of which are components of the pre-mRNA splicing machinery. PPIase assays have shown SpCyp3 and hUSA-CyP to have comparable activity and substrate specificity, but SpCyp3 has a reduced sensitivity to CsA correlating with a difference in the catalytic site. Prp3, Prp4 and Prp18 proteins exist in S. pombe and nuclear localisation of SpCyp3 has been shown, indicating conservation of function between hUSA-CyP and SpCyp3.