The farming of the eucheumatoids Kappaphycus and Eucheuma will be driven by an increase in global demand for carrageenan and natural products, consistent with healthier lifestyles and better living standards. In addition to improvements in farming technique and technology, the use of molecular methods is also essential in the pursuit of greater and more sustainable yields. Over the past few decades, the use of DNA-based molecular markers has greatly improved our understanding on these morphologically plastic seaweeds, stemming from simple yet accurate identification and classification of species, strains or cultivars throughout the world. The application of this knowledge is also crucial in documenting the biodiversity of eucheumatoids, detection of bioinvasion and selection of cultivars with better carrageenan yields, growth rate, disease resistance, tolerance towards climate change etc. The present study highlights the milestones achieved in the molecular taxonomy of Kappaphycus and Eucheuma, as well as general challenges and future recommendations associated with the field.