We have a family that owns 5 business all different tax ID numbers. They use two different branches one in Pa and one in NJ and different people making deposits. Do we need to file a CTR if all of the deposits for one day at all branches total over 10,000.00

The "businesses:" corporatations, partnerships, sole proprietorships...?

Different signers ( all family members) and all incorporated.

FIN 2012-G001 directs that if they are separate legal entities and they are operated as such, you are not to aggregate based on common ownership. (You already indicated the deposits were not made by the same people.)

If you drill back to the 2001 guidance cited you will see that there can be exceptions to that rule when the entities are not treated as separate organizations; e.g. they transfer funds back and forth among them.

I just spoke with the person who does our CTRs and the same bookkeeper deposited money from 3 of the businesses at our NJ office yesterday. A different employee deposited cash into the other two businesses at our Pa office. So we only prepared a CTR for the 3 done at our NJ office by the same employee.

Sounds right to me if "the three" exceeded $10K and "the two" did not; transactions by the same person are subject to aggregation without regard to who they benefit.