The SINEs are short interspersed repetitive elements that propagate in eukaryotic genomes via transcription followed by reverse transcription. Recent genomic surveys have demonstrated that SINEs are active in shaping the architecture of genomes and therefore are powerful markers for studies of phylogeny and population biology. In the present study, a new protocol was developed to apply nonradioactive digoxigenin-labeling system into isolation of SINEs rapidly, safely, and efficiently. The application of this approach is illustrated with discovery of thirteen informative SINEs and a novel member of the t-SINE family in the Omura's whale (Balaenoptera omurai) and sperm whale (Physeter macrocephalus), which is the first record of t-SINE in cetacean. Analysis of subfamily-specific genetic variability and insertions/deletions strongly suggested the existence of some novel CHR-2 SINE subfamilies in the cetacean genomes.