Abstract Seismic site characterization is an important parameter in earthquake hazard assessment for risk mitigation studies, which are essential in engineering design practices and urban planning providing useful information to governmental or private civil protection authorities. Recent advances from site effect studies envisage for the future the importance of incorporating microzonation as a tool for determining resonance prone buildings especially for the most earthquake hazardous municipalities. This study aims to assess the frequencies of vibration of selected masonry and reinforced concrete buildings and to examine potential soil - building resonance in a complex geological setting of the small scale Paleohora Basin (southwest Crete). Ambient noise survey was performed in masonry and reinforced concrete buildings, on soil foundation and on soil at several distances from the base of the selected buildings. The selected public and private (masonry and RC) building constructions are located in the centre of the Basin which is characterized by heterogeneities induced by large scale E-W fault and at rock fractured (of complex orientation and opening of fractures and joints) outcrop site close to the margins of the Basin in the southeast bordered by an NNE-SSW fault. The spatial horizontal to vertical spectral ratio (HVSR) technique using ambient noise reveals that soil-building resonance phenomena could be inferred in the small scale alluvial Paleohora Basin. Two amplified peaks in the centre of the Basin and one amplified peak at the rock fractured outcrop site close to the Basin margins are observed from the data sets. In the centre of the Basin, the amplified peak at medium frequency (3.85–7.11 Hz) is related to the near subsurface irregularities locally induced by E-W faulting, while the low frequency (0.75 Hz) is related to the overlain Quaternary deposits. At the rock fractured outcrop site close to the margins of the Basin the one amplified peak at medium frequencies (2.5 Hz) is related to the fractured limestone outcrop. Weak motion earthquake data following the main earthquake event that occurred near to the southwest coast of Paleohora are recorded in the centre of the Basin (at the schoolyard) and on rock fractured outcrop close to the margins of the Basin. The HVSR of the weak motion earthquake data present in the center of the Basin two amplified peaks at low (0.75 Hz) and medium frequencies (6.56 Hz) and at the rock fractured outcrop site close to the Basin edge one amplified peak at medium frequencies (2.58 Hz). This study conducted in the complex small scale and dense populated Basin, highlights the necessity of incorporating the determination of prone resonance buildings into urban planning for risk mitigation studies, specifically in this earthquake hazardous municipality.