1 - The assessment of quality status of Transitional Aquatic Ecosystems remains a challenge for the ecologists. 2 - Here, we compared the results of two common indices (AMBI - Ecological Groups and BOPA/BO2A -Taxonomic Sufficiency) from samples coming from the north-eastern Atlantic and Mediterranean Sea. Both biotic indices rely on distinct assessments of species sensitivity/tolerance. 3 - Six studies provided the raw data that permitted AMBI and BOPA to be compared. A total 922 data element was available, most of them from the Seine estuary (78%). The database was later divided into three sub-sets: French Atlantic Transitional Waters, Mediterranean Coastal Waters and Mediterranean Lagoons. 4 - Both indices' values demonstrated a strong correlation; however, the BOPA index had a tendency to overestimate the EcoQS compared to the values obtained from AMBI index, mainly due to discrepancies between 'high' and 'good' quality. 5 - New thresholds for BOPA/BO2A index are proposed in order to reduce this overestimation.