Aim. During the 2009-13 period of time joint efforts of eco-eographical faculty of Dagestan State University and the Institute of Applied Ecology of the Republic of Dagestan made large-scale comprehensive studies of flora and fauna of coastal and island ecosystems of the Middle Caspian. The program of the expedition involves the establishment of species diversity of animal and plant life of the population of the study area. The main purpose of this article is to establish the reasons for the high proportion of the indigenous component of the aquatic biota and causal interpretation discovered during research expeditions of the endemism among taxa of an island fauna and flora. Methods. Expedition research covered the western and eastern coast of the Middle Caspian, and the major islands (Chechen Island, Tyleniy, Nordova, Kulaly) of this part of the sea. In faunal studies traditional methods, such as hand-picking, mowing, light traps with quartzemitters, ground traps were used. A new version of the field collecting entomological material was tested: Barber trapsin combination with LED lamps. The last only switched on at night. Location of traps recorded by GPS-navigator. Traps Barbera functioned throughout the expedition period. Removal of the collected material was performed at intervals of 3 days. The need for a causal interpretation of the contemporary configuration of habitat in the species composition of the biota of the study area, has led us to develop a hydrodynamic GIS model of the Middle and North of the Caspian sea. To solve this problem prepared three-dimensional model of the bottom of the Middle and North of the Caspian sea in GIS "Map 2011". The base level of the Caspian sea in this simulation adopted the mark -28 m Matrix, ensuring the functioning of the hydrodynamic GIS model based on approximately twenty thousand marks depths. Results. According to the results of pre-processing of field data set, the General picture of the floristic (higher plants) and fauna (some groups of invertebrates) species diversity (table. 1). It should be emphasized that the biota of the Islands of the Middle Caspian, in General, consists of taxa widely distributed in the Eastern and, to a lesser extent, the Western coast. There are also species the area which goes far beyond the region of the Caspian sea. However, in table 1 preliminary faunal and floral evidence suggests that in the modern biota of the Islands of the Caspian sea found also new to science species, at present unknown in the continental part of the Caspian sea. It taxa species or subspecies rank. That said, modern faunistic or floristic status of this group of species should be considered endemic. Main conclusions . Kind of part of the Caspian autochthonous fauna is largely because of its complex origins. A catastrophic reduction in the area of water surface of the sea takes place with a gradual decrease of its level before -39 m Middle Caspian, since the level of -39 m and -50 m retains approximately the same configuration of the water surface. The decline -100 m and even up to -150 m not accompanied by a catastrophic decline in water surface area of the Middle Caspian sea. Therefore, it should be recognized that the conservation and co-evolutionary development of the unique fauna of the Caspian sea, an important buffer role played by the Middle Caspian. Thus, a causal interpretation of the autochthonous trends and, as a consequence, a high level of endemism taxa of aquatic biota is not straightforward. A different situation with understanding and explanation of the pattern of endemism coastal and especially island taxa. Modern faunistic or floristic status of the new species should be considered endemic. In this group of species identified taxa of species and subspecies rank. The formation and evolutionary stabilization of these taxa requires a time sufficient to cause diagnostically significant features. And this is possible only with the existence in the waters of the Middle and North of the Caspian sea island sushi throughout the Holocene (even during periods of high sea level). Of course that modern configuration of habitat taxa island biota of the Middle Caspian sea due to the magnitude and time duration of transgressive-regressive cycles of the sea and the reasons that determine the direction of these events. In accordance with the nature of these cycles has been a change in the species composition and structural organization of coastal and island communities.