The monitoring of ecosystems alterations has become a crucial task in order to develop valuable habitats for rare and threatened species. The information extracted from hyperspectral remote sensing data enables the generation of highly spatially resolved analyses of such species’ habitats. In our study we combine information from a species ordination with hyperspectral reflectance signatures to predict occurrence probabilities for Natura 2000 habitat types and their conservation status. We examine how accurate habitat types and habitat threat, expressed by pressure indicators, can be described in an ordination space using spatial correlation functions from the geostatistic approach. We modeled habitat quality assessment parameters using floristic gradients derived by non-metric multidimensional scaling on the basis of 58 field plots. In the resulting ordination space, the variance structure of habitat types and pressure indicators could be explained by 69% up to 95% with fitted variogram models with a correlation to terrestrial mapping of >0.8. Models could be used to predict habitat type probability, habitat transition, and pressure indicators continuously over the whole ordination space. Finally, partial least squares regression (PLSR) was used to relate spectral information from AISA DUAL imagery to floristic pattern and related habitat quality. In general, spectral transferability is supported by strong correlation to ordination axes scores (R2
= 0.79–0.85), whereas second axis of dry heaths (R2
= 0.13) and first axis for pioneer grasslands (R2
= 0.49) are more difficult to describe.
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