Natural habitats and ecological systems provide living space for one or more living beings, and they are the source of biodiversity on Earth. Integrity of ecosystems impetuously collapse due to unplanned urbanisation, misuse of lands and excessive consumption of natural resources by human beings. Additionally, monitoring studies are not sufficient to plan preventions. The main aim of this study is to set a precedent by monitoring the damage, the pressure and time-dependent changes, which are caused by highway projects planned without analysing ecosystem flexibility, on natural habitats through the use of remote sensing technique and GIS. The effects of highway projects on habitats are investigated with respect to two different points of view. The first one is that highway projects directly invade and divide habitats. The other one is that highways become centre of attractions for residential and industrial zones, and demand for settlements increases around highways. The research area of this study is the most seriously affected natural area in Aegean region where Izmir-Aydin highway passes through. The changes in the research area in terms of land usage from 1984 to 2014 were analysed by satellite images. The size of industrial and residential zones in the research area was 138 ha in 1984. The size of industrial and residential zone has increased by 1.225% and reached to 1.690 ha as industrial and residential zones became denser throughout the highway. As a result of this study, it was determined that Izmir-Aydin highway has irreversibly split and destroyed substantial part of the natural habitat.