Fish pathogens in marine recirculating aquaculture systems (RAS) can be the source of major costs due to loss of fish. Pathogens can reside in the biofilms of RAS, including in moving bed-biofilm reactors (MBBRs). The microbial communities of periphyton may reduce the number of pathogens in the system, preventing their establishment in the RAS biofilms. In contrast, periphyton may serve as an additional reservoir for pathogens. This study delves into the testing of different aquaculture biofilter combinations such as periphyton with halophytes (H+P), periphyton with moving bed biofilm reactors (P+M), and periphyton only (P2). The microbiome was quantified using 16S rRNA next generation sequencing. The microbiome revealed denitrifiers, ammonia-oxidizing microbes, nitrite-oxidizing microbes, and valuable algae such as Chlorella. Classification of pathogens showed that significantly fewer OTUs containing fish pathogens were found in the periphyton biofilters in comparison to the MBBR (Table 1). To gain higher resolution, the hsp70 gene was used to examine pathogen groups in periphyton biofilters, conventional MBBRs, and in the effluent water from the biofilter.