Ulva is one of the most promising candidates for replacing unsustainable ingredients like animal and plant meals and oils in aquafeeds. Studying Ulva’s dual use in an integrated multi-trophic aquaculture system (IMTA) in water purification and as a protein-rich nutritious ingredient highlights this potential. Still, the high content of indigestible polysaccharides reduces Ulva’s nutritional value and digestibility. It is assumed that genomic knowledge on the ecology of the gut microbiome of an algal-fed sea urchin is essential for developing a bacterial-based process for the decomposition of the algal polysaccharides. For this purpose, research was performed to investigate the structure and functionality of bacterial communities along the digestive tract of the algivorous sea urchin Tripneustes gratilla elatensis. The study combines 16S rRNA amplicon sequencing, bioinformatics, and in vitro trials.