To compare trophic characteristics for pelagic and bottom communities of zooplankton and zoobenthos in the western Chukchi Sea, isotopic composition of carbon and nitrogen (δ13С and δ15N) is determined for three different types of water masses. The main area of the southwestern part of the sea (to the south of 71оN) is occupied by the surface and subsurface water masses invaded from the Bering Sea with relatively high δ13C and low δ15N values. The cold Arctic waters prevail in the northwestern area. The western periphery of the sea is influenced by the water masses from the East Siberian Sea transported by the alongshore Siberian Current, distinguished by significantly lowered δ13С values and somewhat (by 1–3 ‰) increased δ15N values. A stable difference in the carbon isotopic composition between zooplankton and benthic invertebrates is revealed in the southwestern Chukchi Sea that means that the benthic organisms are based mainly on the bottom food chain, with a minimal input of organic matter from the water column. In the area influenced by the water masses from the East Siberian Sea, benthic invertebrates have the lowest values of δ13С comparable to those of zooplankton that is a sign of organic sediments from the water column utilization, partly terrigenous in origin. The role of primary producers for plankton and benthos in the northwestern Chukchi Sea has not been fully elucidated and requires additional studies. However, the main trophic base for the benthic community is assumed there to be organic matter removed from the water column, originated mainly from ice algae.