A serious side effect of climate change is the spread of invasive species (INSP), which constitute a serious and rapidly worsening threat to ecology, to the preservation of natural biodiversity, to the protection of flora and fauna and it can even threaten human population health. These species do not seem to have particular morphological differences, despite the intense variations in their biological characteristics. This often makes their identification very difficult. The need to protect the environment and to safeguard public health requires the development of sophisticated methods for early and valid identification which can lead to timely rational management measures. The aim of this research is the development of an advanced Computational Intelligence (COIN) system, capable to effectively analyze the conditions that influence and favors spreading of invasive species, due to the problem of climate change. Fuzzy Cognitive Maps (FCM) have been used to determine the specific temporal period (in years) in which the rapidly changing average temperature and precipitation in Greece, will become identical to the respective values of the neighboring countries for the period 1996–2015. This climatic evolution will cause spread of INSP met in these Mediterranean countries, to Greece. Separate analysis has been done for several cases of invasive species. The whole analysis is based on climate change models up to 2100.