Macroalgae such as Ulva are living hosts that are known to perform essential roles in marine ecosystems, and are extensively utilised for several aquaculture operations, including in the integrated production of high value goods such as abalone. Intensive aquaculture operations along the coastline release effluent water into the surrounding coastal waters, which has adverse impact on the environment. As a means to bioremediate abalone effluent, several commercial abalone farms in South Africa use Ulva as a biofilter, after which the Ulva may serve as a feed source for the abalone. Advancements in gene sequencing technology has enabled the assessment of large scale 16S rRNA gene libraries of near full-length sequences. However, studies concerning the epiphytic bacterial communities present on macroalgae grown in effluent systems are scarce, and as a result several commercial farmers have become sceptical about utilising effluent grown Ulva as feed. This study addresses the biosecurity implications associated with the use of Ulva as a biofilter and feed within an integrated multitrophic aquaculture (IMTA) system along with the abalone Haliotis midae by assessing the bacterial communities associated with Ulva and its environment. Water and Ulva samples were collected from an integrated abalone farm along the Western Cape of South Africa and assessed via a culture and a non-culture-based approach. Samples were collected from both fertilised seawater tanks and abalone effluent wastewater raceways. The water samples were collected at the inlets and outlets of each tank/raceway and the Ulva was collected from within each system. The culture-based approach utilised three selective media for the isolation and quantification of culturable bacteria, namely Tryptic Soy Agar (TSA, a general growth media), thiosulfate-citrate-bile-sucrose (TCBS) agar (vibrio selective growth media), and Ulvan agar plates, where the primary carbohydrate of Ulva was utilized as the main carbohydrate source. Post isolation, selected bacteria underwent 16S rDNA gene analysis for identification. The non-culture-based approach utilised the next generation Illumina 16S Metagenomic Sequencing platform (MiSeq). Moreover, the Ulva was sequenced using the rbcL gene to identify the species grown in the aquaculture system. Phylogenetic analysis of Ulva suggests that it falls within the U. rigida clade. The sequenced Ulva cultivated at I&J abalone farm shared close similarity with Ulva rigida (KP233772) and Ulva scandinavica (EU484416) on the GenBank database, and hence was referred to with the name of its corresponding molecular synonym, i.e. U. rigida. The culture-based results indicate that bacterial numbers were significantly higher in the raceways receiving abalone effluent water when compared with the Ulva tanks receiving seawater that were fertilized. Bacterial abundance on all three selective media types was higher on the Ulva cultured in the abalone effluent raceways than on the Ulva cultured in the fertilized seawater tanks. Moreover, it was observed that the Ulva has the potential to significantly reduce the bacterial load of abalone effluent water raceways. Rarefaction results from the non-culture-based approach indicate that the Ulva in both the fertilised seawater and abalone effluent raceways had significantly lower bacterial alpha diversity than the water columns themselves. Principal co-ordinate analysis (PCoA) at phylum level showed that bacterial communities on the Ulva and in the water, columns shared similar phyla diversity. Alternatively, PCoA at genus level demonstrated that microbial communities residing on the Ulva (both effluent and fertilised seawater grown Ulva) had significant differences compared with the water samples obtained from both the inlets and outlets of the effluent and fertilised seawater systems. When assessing the differential abundant bacteria on the Ulva, general marine bacteria appear in high abundance and potentially pathogenic bacteria such as Vibrio appear in low abundance. Moreover, the presence of the Ulva within the wastewater seemed to decrease the bacterial abundance of Vibrio within the fertilised seawater tanks as well as the abalone effluent raceways. Despite the presence of potentially pathogenic bacteria within the abalone effluent raceways, the Ulva does not seem to act as a sink for potentially pathogenic bacteria indicating that feeding effluent grown Ulva to abalone is not of significant biosecurity concern. Even though several commercial abalone farmers consider recirculation within aquaculture feed systems high-risk technology, no papers have reported disease outbreaks due to the use of effluent grown Ulva as abalone feed. These results provide a general basis for the dynamic changes in the bacterial community profiles in a commercial abalone farm associated with utilising effluent grown Ulva as a feed additive for abalone. This effort to profile the bacteria associated with Ulva and its environment under fertilised and effluent conditions provides deeper insight on understanding the biosecurity implications of incorporating effluent grown Ulva into abalone feed.