While I have no idea where your problem comes from and I’ve never needed to typeset Russian, replacing mathptmx with newtxmath seems to fix it. The times tag wiki gave me the idea, and while I usually don’t typeset math (and if I did, I wouldn’t use Times), newtxmath seems to be intended as a successor for mathptmx.
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[russian]{babel}
\usepackage{newtxmath}
\begin{document}
оценка эвапотранспирации тростника обыкновенного
\textit{(Phragmites Australis)}
\end{document}

P.S.: This also works with the configuration of your initial MWE.
P.P.S.: Someone more knowledgable in these kinds of font issues might be able to give you a solution without switching packages.
articlewiththesis(all lowercase) in my code, it still works. Is thethesisclass you’re using a custom class? Or do you get any error messages if you compile my code? MWE stands for Minimal Working Example and basically means the least amount of code necessary to reproduce a problem. For some more information, see I've just been asked to write a minimal example, what is that?. – doncherry Jan 27 '13 at 07:46newtxmath. If not, do you use MiKTeX or TeX Live (on which operating system) or something else? – doncherry Jan 27 '13 at 07:54newtxmathshould work right away. – doncherry Jan 27 '13 at 08:05newtxmathandmathptmxhere is that the latter tries to use the font Times (ptm) for text. But it is not available inT2Aencoding, the mechanism of font substitution uses Computer Modern for upright, but tries to substitute Times upright inT2Afor Times italic inT2A. None of them is available (TeXLive 2012). – Jan 27 '13 at 09:37mathptmxmanually, along the lines of e.g. Where do I place my own .sty files, to make them available to all my .tex files?? – doncherry Jan 27 '13 at 16:38mathptmxis wanted for math, one just needs to add after loading it\def\rmdefault{cmr}to counteract its\def\rmdefault{ptm}. Because everything else inmathptmx.styis math mode only. – Jan 27 '13 at 17:17