Selenium (Se) is an essential trace element in vivo. Its biological function is mainly exerted through selenoproteins. Selenocysteine (Sec), the active site of selenoproteins, is incorporated into the protein at an in-frame TGA codon under the guidance of Sec insertion sequence (SECIS) element in the 3-untranslated region (UTR) of the gene. In this work,a method was developed and a series of programs were edited by PERL language to in silico identify selenoproteomes from the genome of domesticated silkworm (Bombyx mori). Out of 18510 annotated genes, 6348 was terminated with TGA codons, 249 containing both in-frame TGAs and SECIS elements in the 3-UTRs. Alignments of those selenoprotein candidates with their cysteine (Cys)-containing homologs revealed that 52 genes had TGA/Cys pairs and similar flanking regions around the in-frame TGAs.Restricted by the patterns of SECIS elements only 5 genes were screened out to fully meet the requirements for selenoproteins. Among them glutathione S-transferase (GST) has been reported as a microbial selenoprotein, the other four are novel selenoproteins annotated as CG6024, CG5195, ATP-binding cassette transporter subfamily A (ABCA), and nuclear VCP-like protein. Derived from the general properties of GST,ABCA and VCP, silkworm selenoproteins may play important roles in redox regulation, Se storage and transportation, as well as cell apoptosis.