The purpose of this paper is a comparative analysis of the tax burden on innovative and non-innovative sectors of manufacturing industry in Russia. We analyze the differences between innovative subsection DL "Manufacture of electrical and optical equipment" and non-innovative section D "Manufacturing" at the Russian regional level using methods of statistical analysis. We found that the level of the tax burden on innovative subsection DL is not lower than on non-innovative section D. It was not discovered though a stimulating effect of taxation on innovative development. Cluster analysis confirmed statistically significant differences in the level of tax burden on subsection DL by regions. We identified several regions with low tax burden. Tax incentives can be used to stimulate industrial development in these territories.