Pushkin's themes in this play are similar to those of Shakespeare's Macbeth. In Boris Godunov we see an additional element of moral ambiguity in that both sides of a power struggle are in some sense illegitimate. In the end we cannot be sure if good or evil has triumphed, or if there is any real difference between the two.

Boris Godunov is a usurper, a man who has had the young heir to the throne of Russia murdered and has himself been elevated to rulership. What then occurs is a phenomenon that has repeated itself throughout Russian history in which a Pretender arises, a man who falsely claims to be the rightful heir whom the people had believed dead. The young monk Grigori crosses the frontier from Russia into Lithuania and Poland and then insinuates himself into the Polish court, raises an army and invades Russia, falsely presenting himself as Dimitri, the rightful Tsar of Russia. In spite of the Pretender's troops being outnumbered, the Russian people, unhappy with Tsar Boris, turn against Godunov and his son, the Prince Feodor, whom the dying Boris has declared the new Tsar. The "False Dimitri" is thus successful in taking over Russia. What we see in Pushkin's treatment of an episode of history is the theme of power lust and the illusion of success that results from it. Like Macbeth, Boris has killed to gain the throne, but also like Macbeth, he is tormented by guilt and is destined to be overthrown due to his misdeeds.

But the other side, represented by the Pretender, is in some way even more illegitimate than Boris. Pushkin's treatment is expressive of Russian patriotism, of the long-standing spirit of Russian resistance to invaders—in this case in the late 1500s and early 1600's (unlike in the previous centuries of the Mongol invasions) an attack from the West, as would happen again and again in history, on through to Napoleon and finally Hitler. The subtext of the Pretender's alliance with Poland is the religious conflict between the Roman Catholics, in Poland and W. Europe overall, and the Eastern Orthodox Russians. Pushkin's point may be ultimately that even if Boris has committed murder to gain the throne, he is still a more rightful ruler, supporting and upholding Russian sovereignty and religion, than the Pretender is.

Two other themes worth noting are the fickleness of the people, the fact that the emotions of "the mob" will turn on a dime given the right conditions. The Russians are given an opportunity to overthrow Boris, who is widely disliked, and they take it, siding with the invaders in the apparent belief that the Pretender is the legitimate heir. It is not unlike the behavior of the Roman mob as Shakespeare shows it in Julius Caesar. But a second, larger issue Pushkin raises concerns the nature of power in general. Is it ever truly legitimate? Or is it simply based on manipulation and deceit, whoever is in charge?