Where do I get bees from?

We already have an answer for a similar question which you can see here:
How to get bees to make a candle?

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You start to collect bees by first growing the flowers that sprout up from the seeds given by the watering cans.

Watering Can=> Seeds (merge seeds to upgrade to flowers)=> Once at the last of the flower upgrade you have to wait until it's ready to be clicked; once clicked you get bees starting from a single bee, to a double set of bees, to a honeycomb, tray of honey, etc.