Antiphospholipid syndrome (APS), also known as Hughes syndrome, is a systemic autoimmune disorder characterized by recurrent thrombosis and pregnancy complications, accompanied by the presence of antiphospholipid antibodies (aPLs). These antibodies target anionic phospholipids or protein–phospholipid complexes within cell membranes, contributing to the underlying mechanisms of the disease. Although anticoagulation therapy remains the cornerstone of APS management, it often fails to prevent complications, particularly in obstetric and thrombotic cases. As autoimmune diseases become increasingly linked to alterations in the gut microbiome, this study investigates the complex interaction between gut bacteria and immune modulation in APS. We explore how disruptions in the gut microbiome may influence the development of autoimmune conditions, with a specific focus on APS. By identifying key microorganisms potentially involved in this gut–immune axis, we aim to provide insights into novel preventive and control approaches. Future research should focus on harnessing the gut microbiome to develop more effective treatments that target both the immune system and microbial populations in APS patients.