A prebiotic is defined as “a nondigestible food ingredient that beneficially affects the host by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon, and thus improves host health.” They should also 1) be resistant to gastric acids, enzymatic hydrolysis and gastrointestinal absorption 2) can be fermented by intestinal microflora and 3) selectively stimulates the growth and/or activity of beneficial intestinal bacteria required for good health. The use of prebiotics for shrimp is relatively recent and knowledge of known prebiotics for shrimp is scant. Inulin and mannoprotein, when used as prebiotics, have been shown to enhance survival rates in shrimp. In this study, agar was added to a commercial shrimp feed to assess its effects on the gut microbiome and gut histology of Pacific Whiteleg Shrimp (Litopenaeus vannamei). Shrimp were fed with either agar-supplemented or unsupplemented commercial shrimp feed for 30 days and then sacrificed. Sections of the mid-gut were isolated and its contents were collected for DNA extraction, bacterial plate count and then fixed in buffered formalin, processed and stained with hematoxylin and eosin for histological examination. DNA extracted from gut content was subjected to 16S rDNA sequencing. Data revealed differences in the abundance of certain bacterial taxa between the agar-supplemented and unsupplemented groups. At the end of 30 days, shrimp fed with unsupplemented feed had a higher percentage of Flavobacteriia (13.5%) and Alphaproteobacteria (6.1%) compared to shrimp fed with agar-supplemented feed (Flavobacteriia 4.6%; Alphaproteobacteria 1%). However, shrimp on the agar-supplemented diet had a higher population of Gammaproteobacteria (93.3%) compared to the unsupplemented diet (75.8%). Both groups had a significant reduction in the population of Mollicutes by day 30 (agar-supplemented 0.2%; unsupplemented 3.1%) compared to shrimp at day 0 (18.7%). Moreover, total bacterial counts on De Man, Rogosa and Sharpe agar (MRS), selective for lactic acid bacteria, were higher in shrimp receiving the agar supplement (1.5 x 103 CFU/g mid-gut) compared to shrimp without agar supplement (5.92 x 102 CFU/g mid-gut). No differences in intestinal cell morphology could be detected from histological examination of the mid-gut. Our data suggests that supplementation of shrimp diets with agar may positively influence the population of potentially beneficial bacteria in the gut and that it has no negative effects on the cellular integrity of the gut.