The FK506-binding proteins (FKBPs) perform an extensive variety of functions in numerous organisms from archaea to humans. The FKBPs are distinguished by their peptidyl-prolyl cis-trans isomerase (PPIase) activity and ability to bind the immunosuppressive drugs FK506 and rapamycin. Here, we report the isolation and characterization of FKBP45, a novel member of the FKBP family obtained from U1 small nuclear RNA (snRNA) binding assays using Bombyx mori nuclear extracts. The protein, an apparent orthologue of FKBP46 from the armyworm, Spodoptera frugiperda, was found to associate with U1 stem-loop I RNA in vitro. The FKBP45 cDNA was isolated and the genomic sequence was characterized, including the positions of exon/intron junctions and consensus splice sites. Using bioinformatics, transcription factor consensus binding sites were identified and subsequent Western blotting from developing eggs indicate that FKBP45 is differentially expressed during embryogenesis. A database was assembled using more than 1,800 available FKBP amino acid sequences and pairwise sequence alignments revealed several putative FKBP45 orthologues in various species. Analysis of these sequences revealed the position of an RNA binding domain within this new protein. In addition, FKBP45 possesses similar characteristics to several potential orthologues, including the presence of bipartite nuclear localization signals (NLSs) and phosphorylation sites.