The ancient city of Perinthos (Marmaraereglisi/Tekirdag/Istanbul), where researched with a systematic multidisciplinary archaeological project were initiated by the Ministry of Culture and Tourism in 2021, has the potential to accommodate both marine and land-based multidiscipline studies in a comprehensive approach. To investigate the traces of archaeological remains, an integrated geophysical survey was designed. As part of the project, a comprehensive multi-beam bathymetry study was carried out in the city's offshore zones, while geophysical studies were carried out on land. The bathymetry study aims to model and investigate the detailed seafloor morphology of the coast of the Perinthos. The seafloor morphology modelled using high-precision data gave us a unique opportunity to investigate the mysteries of the ancient city of Perinthos. Multi-beam bathymetry data in over 1000 hectare acquired with 400 and 700 kHz central frequency sensors. Throughout the data processing procedure, the ¨International Hydrographic Organization Standards for Hydrographic Survey¨ were adhered to. Finally, morphological imagery of the seafloor was obtained. The resolution of these images, varies between 10 cm and 1 meter depending on the depth. This study is a significant contribution to the high-resolution identification of ancient cultural heritage through the multi-beam bathymetry in marine archaeological sites.