SRAP and TRAP are two kinds of newly developed molecular marker systems with the advantages of simplicity, high throughput, numerous co-dominant makers, highly reproducibility and ready to sequence, especially preferential targeting ORFs. The principle and protocol of SRAP and TRAP, which were developed in Brassica and Helianthus crops firstly, are introduced in the paper. Primer design is a key step for SRAP and TRAP, and some F-and R-primers were developed. Unlike SRAP technique, the TRAP requires cDNA or EST sequence information for fixed primer development. The annealing temperature is 35 degrees in the first 5 cycles and 50 degrees in the subsequent 30~35 cycles. The amplicons can be separated by polyacrylamide or agarose gel, and detected by autoradiography, silver or EB staining. SRAP and TRAP are applied in germplasm genetic diversity analysis, genetic map including transcriptome map construction, important trait gene tagging and gene cloning in many crops.