The paper proposes a geoinformation approach for biodiversity and vulnerability mapping for North Caspian biota on the base of mathematical model. Maps are built using probabilistic description of biota habitat that allows to take into account the uncertainty of their borders. Geoinformation model is based on mapping of 175 objects of the Northern Caspian biodiversity. As an example the article provides the mapping of habitats of some species of biota. Vulnerability maps, in addition to describing biodiversity considers also «the importance» or «the vulnerability» of each element of the biota that allows to describe in a quantitative sense the state of the ecosystem as a whole more subtly. As a result, the series of biodiversity and vulnerability maps for each month have been obtained, reflecting seasonal variation during the calendar year. These maps can be used to assess environmental risks, including the carrying out of oil operations in the sea, as well as during the monitoring of the environment of the Northern Caspian.