Analytical techniques to track plant genes in the environment and the food chain are essential for environmental risk assessment, government regulation and production and trade of genetically modified (GM) crops. Here, I review laboratory techniques to track plant genes during pre-commercialization research on gene flow and post-commercialization detection, identification and quantification of GM crops from seed to supermarket. At present, DNA- and protein-based assays support both activities but the demand for fast, inexpensive, sensitive methods is increasing. Part of the demand has been generated by stringent food labeling and traceability regulations for GM crops. The increase in GM crops, changes in GM crop design, evolution of government regulations and adoption of risk-assessment frameworks will continue to drive development of analytical techniques.