This chapter focuses on the regulation of synthesis and accumulation of the essential amino acids lysine and threonine in plants and in seeds as autonomous organs, and approaches to increase the content of these essential amino acids in seeds. Information on the regulation of synthesis of other essential amino acids in plants can be obtained from other excellent reviews. The pattern of free lysine accumulation in seeds from transgenic plants expressing the bacterial insensitive dihydrodipicolinate synthase was entirely different from that of free threonine accumulation in plants expressing the bacterial insensitive Aspartate Kinase. Although the catabolism of lysine has been studied quite extensively in microorganisms, fungi, and animals, very little is known on the pathways and regulation of lysine catabolism in plants. Molecular studies suggest that the levels of free amino acids, particularly lysine, in plant seeds may be determined not only by the efficiency of their synthesis but also by their stability in the free pool.