Belief
The conflict between belief and unbelief dominates Marlowe's play. In the sixteenth century the concept of atheism could be defined as both a denial of the existence of God and also a denial of the goodness of God. Faustus uses the idea of 'a mighty god' as an alternative to the Christian God. So while modern audiences wouldn't consider him an atheist, an Elizabethan audience would. In addition, while he is sceptical about God, he seems to believe that he has a soul. Paradoxically this aligns him with some aspects of conventional theology but not others. His belief system is shaky and suspect; he is constantly moving from one opinion to another, unable to root himself. His sense of identity wavers, shown in his use of his own name instead of the personal pronoun, as if he is standing outside himself looking helplessly on.
Religion
The succession of Queen Elizabeth to Mary in 1558 saw Catholicism outlawed in England. The Pope was described as the Antichrist, the Catholic Church as the 'Whore of Babylon', and Catholic forms of worship, in particular the Latin Mass, treated with disgust and terror. Repressive laws and taxes were introduced in order to re-educate the public and turn them towards Protestantism. The fear of invasion and the war with Spain intensified the revulsion. Priests who failed to attend Protestant services were arrested - if they were caught administering the forbidden Catholic rites they could be tortured to death. However, the reign of Elizabeth did not feature more violence than Mary's; religious dissent was met with execution in both.
Marlowe placed Faustus in the Martin Luther's home university of Wittenberg, whose teachings were the basis for the formation of early sixteenth century Protestant Anglicanism. That Faustus should mock the Pope suggests Marlowe is satirizing Catholicism; an Elizabethan audience would quickly be ready to laugh at these jokes. His use of Latin in his spells suggests the Latin of the Catholic Mass, and that Marlowe is setting up the idea that Catholicism is no more than a trick of the Devil's. In consideration the play certainly seems to be a diatribe against the Catholic religion.
The dominance of mainstream Anglicanism during Elizabeth's reign was put under stress by the Puritan religion. The Puritan sect, with its emphasis on free speech and independent thought, undermined the officially prescribed homilies and services set down in the Book of Prayer, ordained by Elizabeth's Government. Rather than conformity to authority, the religion preached individual obedience to one's own conscience instead. This was deemed dangerously subversive, and was a source of anxiety to those in positions of power. Shepherd draws attention to the way Marlowe's plays "often show scenes or stories in which …individual speech is repressed or in which official speech making is viewed critically". Faustus is seen as struggling between an ideal of Puritan individualism, and the need to conform to imposed structures.