This application note details how the Agilent 2100 Bioanalyzer was used in polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) fragment analysis for fish species identification. A 464bp cytochrome-b target sequence, found in all vertebrate fish, was first amplified and then digested with restriction enzymes. The fragments were resolved on the DNA 500 LabChip®, allowing simple comparison with authentic species profiles due to the accuracy of fragment size determination. Use of the Bioanalyzer offered significant benefits over traditional gel electrophoresis and DNA staining techniques for PCR-RFLP fragment analysis.