Caltrans officials say a hive, with about 15,000 bees was found in a eucalyptus tree along El Camino Real at Hillside Drive.
Some trees had to be cut down after the winter storms damaged them.
VIDEO: San Jose neighbor creates buzz over his plans to increase honey bee population
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Crews were working on the trees Monday while bee experts relocated the hive.
Beekeepers say it's been a tough job trying to remove the bees from the trees so far.
"In this case where it's way too big, what we do is come the day before, and we seal up the tree... Unfortunately, it didn't work on this job," said beekeeper Raymond Wolfgramm.
El Camino Real was closed between Hillside Drive and Mills Avenue until around 5 p.m. Monday while crews wrapped up.
All the bees are being relocated to a local farm.