Abstract Introduction Filifactor alocis is a newly appreciated member of the periodontal community with a strong periodontal disease correlation. Little is known about the survival mechanisms by which F. alocis copes with oxidative stress and establishes the infection within the local inflammatory microenvironment of the periodontal pocket. The aim of this study is to investigate if F. alocis putative peroxiredoxin/AhpC protein FA768 may constitute an alkyl hydroperoxide reductase system utilizing putative thioredoxin reductase protein FA608, and putative thioredoxin/glutaredoxin homolog FA1411/FA455. Methods FA768, FA608, FA1411 and FA455 proteins from F. alocis were expressed and purified from Escherichia coli . Insulin and 5,5‐dithio‐bis‐2‐nitrobenzoic acid (DTNB) reduction assays were performed to determine if purified FA1411 and FA455 proteins could be a substrate for FA608. The peroxidase activity of FA768 was examined by measuring its ability to reduce hydrogen peroxide (H 2 O 2 ) with FA608 and FA1411/FA455 provided as the reducing systems. Further, the hydroperoxide substrate specificity of FA768 was analyzed by monitoring the NADPH oxidation in the presence of different peroxides, including H 2 O 2 , cumyl hydroperoxide (CHP), and tert‐butyl hydroperoxide (t‐BHP). Results In this study, we have demonstrated the existence of a functioning thioredoxin‐dependent alkyl hydroperoxide system in F. alocis . This system is comprised of a thioredoxin reductase (FA608), a thioredoxin/glutaredoxin homolog (FA1411/FA455), and a typical 2‐cysteine peroxiredoxin/AhpC (FA768). FA608, together with FA1411/FA455, can function as a thioredoxin reductase system to reduce insulin, DTNB, and FA768. FA455 is a glutaredoxin‐like protein with thioredoxin functions in F. alocis . Both the FA768/FA608/FA1411 and FA768/FA608/FA455 reductase systems were NADPH‐dependent and exhibited specificity for broad hydroperoxide substrates H 2 O 2 , CHP, and t‐BHP. Conclusions This is the first study of a thioredoxin dependent alkyl hydroperoxide system from a periodontal pathogen. This system is proposed to protect F. alocis against oxidative stress due to the likely absence of a catalase or an additional peroxiredoxin homolog.