In an attempt to authenticate commercial frauds in fresh products of Atlantic salmon ( Salmo salar) by being adulterated and substituted with those of rainbow trout ( Oncorhynchus mykiss), two molecular tools, AFLP (amplified fragment length polymorphism) and DGGE (denaturing gradient gel electrophoresis) were explored here. A species-specific SCAR (sequence characterized amplified region) marker for rainbow trout ( O. mykiss) was developed based on AFLP analysis. In addition, DGGE was utilized to discriminate Atlantic salmon ( S. salar) from rainbow trout employing a fragment of the mitochondrial cytochrome b gene. Analysis of experimental mixtures demonstrated that the detection sensitivity of AFLP-derived SCAR is higher than that of DGGE. In order to ascertain commercial frauds are fabricated by the adulteration or substitution of rainbow trout, DGGE analysis of cytochrome b gene should be combined because only one species-specific SCAR just for rainbow trout was obtained in this study.