The insects in the latest incident were taken from a wooded area in Craichie by Forfar, Angus, between midnight on Saturday March 29 and midnight on Sunday April 20.
Police Scotland said three queen bees, approximately 45,000 working bees and three honeycomb frames were taken in the raid.
Whoever took the bees would have had specialist knowledge about handling them, officers said.
News of the latest raid came after police last week appealed for information about the theft of bees from a farm in Coupar Angus, Perthshire.
That theft was said to have happened between 11am on Saturday April 19 and 12pm the following day.
Six queen bees, a "large quantity" of working bees and 18 honeycomb frames were taken.
Police are not ruling out the possibility that the two incidents are linked.
Officers at Police Scotland's Tayside Division said anyone with information about either theft should contact them on 101 or Crimestoppers on 0800 555 111.