Between 20 September and 10 October, 15 bikes in a storage area in Bainfield Place and surrounding business premises in the Fountainbridge area were stolen.
The teenagers, aged 15 and 18, have been charged with a total of 18 offences.
PC Simon Wotton, of Police Scotland, said: "Three bikes worth around £1,000 each have been recovered so far."
Two teenage boys have been charged with the theft of £10,000 worth of bikes in Edinburgh.