The present study deals with wood charcoal macroremains recovered from the archaeological sites of Akrotiri, Thera and Heraion, Samos. The main objectives of this thesis are to examine first the transformation of the vegetation in the surroundings of the aforementioned sites overtime and then to account for the reasons behind these changes; finally the taxa preferred by the inhabitants in the construction of their buildings are scrutinized to elucidate the reasons for their choices. The samples studied from Akrotiri date from the Early Cycladic to the Late Cycladic I periods, while those of Heraion are from assemblages dated between the Chalcolithic to the Middle Bronze periods, as well as the Archaic and the Roman periods. In both cases, the anthracological diagrams indicate a transformation of the natural landscape towards a more controlled environment, at least from the Middle Bronze period onwards. The inhabitants exploited the surrounding vegetation to collect fuel wood and probably edible fruits, which latter habit led to the systematic management of fruit-bearing taxa, like Olea europaea and Prunus amygdalus. The surrounding vegetation was also the main source of construction timbers, which were selected first according to their availability and secondarily with regard to their individual physical properties. The extensive architectural study by Palyvou (1999), along with the systematic sampling and the analysis of anthracological specimens from the interior of the buildings of Akrotiri, has allowed suggestions to be made on the taxa used for the construction of the wooden floors of the upper storey, the infrastructure of the walls, and the windows and doors. The main species used were Olea europaea, Pinus type brutia/halepensis, Quercus type evergreen and deciduous. Exceptional here is the recovery of exogenous taxa, Cupressus sempervirens and Castanea sativa, which were also used in constructions. The anthracological samples recovered from the interior of the houses of Heraion are related more to their wooden roofs. The study of relevant contexts dated from the Chalcolithic to the Middle Bronze period allowed comparisons to be made between the taxa used at each period. Overall, the taxa mostly utilized were Olea europaea, Fraxinus sp., and Quercus type evergreen and deciduous.