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We studied the influence of microclimatic parameters (air temperature and air humidity) on certain natural habitat islands (karst sinkhole and sand dune slack) and on their plant species composition and vegetation pattern in Hungary. Vegetation data together with topographic variables were collected along transects to reveal the vegetation patterns on the slopes. Microclimatic parameters were measured with wireless sensor motes equipped with air temperature and humidity sensors. Interactions were examined using distance-based redundancy analysis. We found that the species composition of natural habitat islands varied markedly within short distances, depending on the prevailing microclimatic conditions. Elements of microclimate (daily, daytime, and nighttime averages) have different effects on vegetation pattern and species composition. The observed patterns can be interpreted based on our knowledge on the structure of plant communities and on the role of geomorphology. 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