In recent years, development of sustainable and ecological food production has gained worldwide interest. It seems clear that this phenomenon is causing changes in aquaculture-focused research, with the development of new integration systems. However, it is still necessary to understand different aspects involved in integrated systems, including co-culture systems such as shrimp and seaweed. This study evaluated the effect of green seaweeds as food source on white shrimp Penaeus vannamei intestinal bacterial communities. Shrimp were evaluated after a 4-week experimental trial under different diet treatments: fed with only pellet (P), only Ulva clathrata (UC), U. clathrata + pellet (UCP), only Ulva lactuca (UL), and U. lactuca + pellet (ULP). In terms of growth and survival, no significant differences (P > 0.05) were found between ULP and UCP treatments compared with the control (P). Analysis of the bacterial biota of shrimp intestine revealed significant differences on community composition in ULP, UL, and UC compared with the control (P) (P < 0.05). We found that Proteobacteria is the most abundant phylum in all treatments, followed by Bacteroidetes for UC, UCP, and UL and Actinobacteria for P and ULP treatments. Shrimp fed only with seaweed U. lactuca (UL, ULP) had a significantly higher abundance of Rubritalea, Lysinibacillus, Acinetobacter, and Blastopirellula, and for U. clathrata treatments (UC, UCP), it was Litoreibacter. Relative abundance of Vibrio was higher in the control (P), showing a decrease in UC and UL treatments. Our findings provide a better understanding of integrated aquaculture systems, specifically those utilizing seaweed as natural feed source.