The genera Gracilaria and Gracilariopsis represent important marine bio-resources. Exploitation has experienced strong growth over the last decade, and Gracilariaceae is now the third-largest farmed seaweed in terms of volume production globally. Due to global changes and anthropogenic impact on coastal areas, Gracilariaceae, like many other cultivated seaweed species, face challenges, such as increased frequency and severity of heat waves, pathogenic epiphyte, disease and pest outbreaks, and overgrazing. These changes could have a huge impact on Gracilaria and Gracilariopsis farming, and achieving large-scale sustainable seaweed farming could be a challenge since strains cultivated nowadays were not selected to withstand these new environmental conditions. To ensure the future of these crops, it is urgent to select new, more resistant, and resilient strains. A prerequisite to attain this goal is the access to a vast portfolio of genetic diversity within species already domesticated and cultivated but also for close-by species that have not yet been cultivated commercially but represent good candidates for future cultivation and agar extraction, a good understanding of the genetic basis of traits of economic interest, and the development of long-term breeding programs based on marker-assisted selection (MAS). However, due to poor farm management and unregulated overharvesting of natural populations, genetic resources seem to be currently dwindling. This chapter aims to summarize the main threats to aquaculture faced by various species of commercial importance of the genus Gracilaria and Gracilariopsis. A review of the current state of genetic resources, the drivers affecting them, and what management and conservation (both in situ and ex situ) plans have been developed to protect them is also included. We discuss how the development of MAS and other genetic tools can now help in ameliorating and future-proofing Gracilariaceae crops.