Coral reefs are keystone species providing nutrients and shelter for many marine organisms. Coral restoration continues to face many challenges involving various external factors such as pollution, acidification, and overfishing. These ecosystems are primarily threatened by ocean warming leading to coral bleaching, which disrupts a symbiotic relationship by expelling algae. This is a unique and crucial symbiotic relationship with Symbiodiniaceae, where both exchange nutrients. If dysbiosis persists, coral becomes more vulnerable leading to death. By genetically engineering the algae cells, we can combat their expulsion under extreme conditions. There are many challenges with dinoflagellate modification, so variations of genetic transformation will be explored. Transformation tools have traits of green chemistry because the selection process inhibits growth of any cells with unsuccessful genome integration, preventing unnecessary biowaste. Once a transformation method is established, we anticipate modifying the cell genome with genes that are temperature or pH tolerant, among others. Before coral death, there is also an opportunity to restore these organisms through delivery of algae into the endosymbiont. Using a biocompatible and digestible hydrogel, we propose encapsulating algae cells for coral intake. Hydrogels are designed using proteins that dinoflagellates will not only be able to ingest but also recognize as sustenance. Green chemistry principles are incorporated into hydrogel synthesis because each component is completely used in formation, then broken down enzymatically within the coral, leaving no waste. By combining genetic engineering and biomaterial synthesis we can preserve coral reef ecosystems. Materials for both approaches require minimal hazardous reagents, while future directions for hydrogel synthesis will promote green chemicals only, and genetic transformation will explore small scale cultures to maintain energy efficiency beyond the trial and error phase.