Antiphospholipid syndrome (APS) otherwise known as Hughes syndrome is a systemic autoimmune disease typically linked with characteristic features like thrombosis and pregnancy morbidity with the presence of antiphospholipid antibodies (aPLs). Although anticoagulation is the current flagship treatment for APS, there are reports indicating a considerable failure following this regimen in a significant number of obstetric APS and thrombotic APS cases. Antiphospholipid antibodies (aPLs) bind anionic phospholipids or protein-phospholipid complexes within the cell membrane. Here, we gave a general overview of the biology of APS and the human gut microbiome, our current understanding of the gut bacteria-immune axis in autoimmunity focus on the potential link to APS, highlighting the implicated microorganisms in this context, and proposing recommendations on future therapeutic development.