What can each do that the other cannot? Is it wise to stick to a particular one or are there use cases for each?

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    Missionaries, as Ktash points out, become decent late game because Great Prophets cost so much more, but Great Prophets can usually convert a city to your religion in a single turn. It could take multiple missionaries to do that, and if you don't have open borders with that player, it can be incredibly difficult to get your missionaries to their large cities (or any city with large borders) without them dying to attrition. – FreeAsInBeer Oct 13 '14 at 13:18

Great Prophets are much more powerful (as their name would suggest). They can found and enhance religions, construct holy sites, and spread their religion 4 times. And when converting units, they can also remove existing religions from the city as well.

Missionaries can only spread religion, and they can only do so 2 times (3 if you have the Great Mosque of Djenne). Also, if you end your turn with a missionary in a rival's territory where you do not have an open borders treaty, they lose 25% of their maximum conversion power. If they lose all their power, they disappear (called attrition).

Both of these units can enter into another player's territory without starting a war, even if you don't have an open borders treaty with that country.

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  • 5
    Perhaps worth adding: The other significant difference is that missionaries get easier to generate as the game goes on (as they cost a fixed amount of faith, and you're generating more), while Great Prophets stay difficult and may get harder (as each new Great Prophet takes more faith to produce). This is the reason not to just use Great Prophets for everything! – Flyto Oct 13 '14 at 8:44
  • IIRC when you use a Great Prophet to spread a religion, all other religions in the target city are removed, making your dominant in that city. – Adeese Oct 13 '14 at 13:05
  • @Adeese Yes, Great Prophets remove all other religious followers in that city, but don't always make their religion the dominant one. Sometimes it takes two uses of their Spread Faith ability to become the dominant religion. – FreeAsInBeer Oct 13 '14 at 13:14

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