In bacteria and archaea, many functionally related genes are organized into operons in order to be transcribed and translated simultaneously. Operons are rarely seen in eukaryotes except for the Trypanosome and nematode, in which they are first transcribed into polycistronic transcripts but then processed into individual mature mRNAs. Recently, several researchers described the findings of polycistronic transcripts also in insects, which revised the previous thoughts that polycistronic genes were absent or few in eukaryotes. Similar to prokaryotic operons, the encoded peptides or proteins are translated simultaneously from a single polycistronic mRNA, providing new insights into the evolution of polycistronic genes. More interestingly, one type of the newly identified polycistronic genes encodes biologically important peptides composed of as few as 11 amino acids. These new findings will spur scientists to identify more small peptides in genome-solved organisms, and change the definition of coding sequences in genomic annotation.