. Stroke affects the expression of muscle synergies underlying motor control, most notably in patients with poorer motor function. The majority of studies on muscle synergies have conventionally approached this analysis by assuming alterations in the inner structures of synergies after stroke. Although different synergy-based features based on this assumption have to some extent described pathological mechanisms in post-stroke neuromuscular control, a biomarker that reliably reflects motor function and recovery is still missing.. Based on the theory of muscle synergies, we alternatively hypothesize that functional synergy structures are physically preserved and measure the temporal correlation between the recruitment profiles of healthy modules by paretic and healthy muscles, a feature hereafter reported as the FSRI. We measured clinical scores and extracted the muscle synergies of both ULs of 18 chronic stroke survivors from the electromyographic activity of 8 muscles during bilateral movements before and after 4 weeks of non-invasive BMI controlled robot therapy and physiotherapy. We computed the FSRI as well as features quantifying inter-limb structural differences and evaluated the correlation of these synergy-based measures with clinical scores.. Correlation analysis revealed weak relationships between conventional features describing inter-limb synergy structural differences and motor function. In contrast, FSRI values during specific or combined movement data significantly correlated with UL motor function and recovery scores. Additionally, we observed that BMI-based training with contingent positive proprioceptive feedback led to improved FSRI values during the specific trained finger extension movement.. We demonstrated that FSRI can be used as a reliable physiological biomarker of motor function and recovery in stroke, which can be targeted via BMI-based proprioceptive therapies and adjuvant physiotherapy to boost effective rehabilitation.