A hydrographic survey of the southwestern coastal margin of Lesvos Island (Greece) was conducted by the Naftilos vessel of the Hellenic Hydrographic Service. The results have been included in a bathymetric map and morphological slope map of the area. Based on the neotectonic and seismotectonic data of the broader area, a morphotectonic map of Lesvos Island has been compiled. The main feature is the basin sub-parallel to the coast elongated Lesvos Basin, 45 km long, 10–35 km wide, and 700 m deep. The northern margin of the basin is abrupt, with morphological slopes towards the south between 35° and 45° corresponding to a WNW-ESE normal fault, in contrast with the southern margin that shows a gradual slope increase from 1° to 5° towards the north. Thus, the main Lesvos Basin represents a half-graben structure. The geometry of the main basin is interrupted at its eastern segment by an oblique NW-SE narrow channel of 650 m depth and 8 km length. East of the channel, the main basin continues as a shallow Eastern Basin. At the western part of the Lesvos margin, the shallow Western Basin forms an asymmetric tectonic graben. Thus, the Lesvos southern margin is segmented in three basins with different morphotectonic characteristics. At the northwestern margin of Lesvos, three shallow basins of 300–400 m depth are observed with WNW-ESE trending high slope margins, probably controlled by normal faults. Shallow water marine terraces representing the last low stands of the glacial periods are observed at 140 m and 200 m depth at the two edges of the Lesvos margin. A secondary E-W fault disrupts the two terraces at the eastern part of the southern Lesvos margin. The NE-SW strike-slip fault zone of Kalloni-Aghia Paraskevi, activated in 1867, borders the west of the Lesvos Basin from the shallow Western Basin. The Lesvos bathymetric data were combined with those of the eastern Skyros Basin, representing the southern strand of the North Anatolian Fault in the North Aegean Sea, and the resulted tectonic map indicates that the three Lesvos western basins are pull-aparts of the strike-slip fault zone between the Skyros Fault and the Adramytion (Edremit) Fault. The seismic activity since 2017 has shown the co-existence of normal faulting and strike-slip faulting throughout the 90 km long Lesvos southern margin.