Living organisms at all stages of evolution, from archaea and bacteria to humans contain inorganic phosphorus compounds: orthophosphate, pyrophosphate and inorganic polyphosphates. Cell polyphosphates operate in a variety of processes such as reservation of phosphate and energy, detoxification and binding cations, formation of specific membrane channels, formation of cell walls, control of gene expression and regulation of the activity of certain enzymes, adaptation to stationary phase and stress. Aim of our work was to study the pole of the ortho - and polyphosphates into the naphthalene biodegradation process by a strain Pseudomonas putida BS3701. It has been shown that the limiting concentration of phosphate into the growth medium with glucose or naphthalene for strain P. putida BS3701 is 0.1 mM and 0.4 mM, respectively, despite on the fact that the products of naphthalene biodegradation are not subjected to phosphorylation. Under the lack of phosphate in the medium (0.4 mM) salicylate as the intermediate product of naphthalene biodegradation accumulates into medium and the activity of key enzymes of naphthalene biodegradation changes. Concentration of polyphosphates in cells is the lower when the strain being cultivated in the medium with naphthalene in compared contras to the medium with glucose (17 mM and 60 polyP/ liter of the medium, respectively), under the condition of phosphate limit in the culture medium. At the excess of phosphate differences of polyphosphate concentrations are not observed neither for glucose nor for naphthalene. Fluorescence microscopy revealed differences in the structure and localization of polyphosphates in cells. Thus, a low concentration of phosphate in the culture medium results in insufficient accumulation of polyphosphates in cells of bacteria P. putida, which was manifested in a change in the activity of enzymes and salicylate transport in cells.