The origin of new exons is an important mechanism for proteome diversity. Here, we report the recurrent origination of new exons in mammalian chromodomain Y-like (CDYL) genes and the functional consequences associated with the acquisition of the new exons. Driven by positive selection, the newly evolved longer peptide exhibits weaker transcription repression activity and attenuates the repression activity of the old form, suggesting that the acquisition of the new exons is functionally significant.