The alarm at the Edinburgh Cycle Company on Granton Road went off at 2.20am yesterday.
Witnesses said they heard glass breaking being before seeing two men cycling away on bikes from the shop.
A Giant Trance X0 29er, worth around £3500 – one of only two in Scotland, and a Diamondback Sortie 3, worth around £2400 were taken in the robbery.
The thieves also stole money from the till.
The owner of the shop, Neill Hope, has offered a reward on Facebook for the recovery of the bikes.
He said: “The thieves stole the two most expensive bikes in the shop and the contents of the till.
“There will be a reward for the recovery of the bikes or information that leads to the thieves getting caught.”
Lothian and Borders Police are appealing for witnesses to the break-in and are asking anyone with information to contact them on 0131 311 3131.