The images were caught on CCTV cameras installed at St Peter and St Paul's Church in Uppingham after a series of break-ins.
The men can be seen loitering in the church before moving the flowers to the doorway. After appearing to look out of the church doors they then leave with the flowers.
It happened at 1.30pm on Friday last week.
Police are appealing for information, but the incident has outraged the church.
Canon Stephen Evans said: "Have you ever heard of people stealing wedding flowers before? Gone are the days when people respected churches."
Canon Evans said: "While we have gone to every possible expense in securing the property, our main aim is to keep the church open.
"But the constant damage and theft raises questions as to just how long this is going to be possible.
"We have a flower festival this weekend and my great fear is they could steal flowers for that."
The flowers, worth about £125, were dropped off by a friend of the couple getting married on Saturday.
Valerie Morse, who co-ordinates the church flower arrangements, was there in the morning, but when she returned at 3pm they had gone.
At first she thought the flowers had been moved somewhere else but at 4pm the woman who had planned to arrange flowers for the happy couple, contacted her to say they were missing. Replacement flowers had to be bought.
Mrs Morse said: "I am furious someone could come in and
take them. They must have been watching.
"It has made us quite nervous. There is always someone in the church now – it will be manned."
In September lead worth £12,500 was stolen from the Market Place church's roof, which has just been replaced; a silver gilt box given to the church by Uppingham School and worth £700 was taken in March, and on Easter Monday this year someone dug out the wall safe and took it and its contents.
Insp Sarah Cox of Rutland police said: "We are investigating this matter and it is terrible that the couple could have had their day ruined by this theft. We are working with both them and the family to investigate this crime."
Police are appealing for witnesses to come forward. Anyone who recognises the men or who has any information should ring PC Adam Ploszczanski on 0116 222 2222.