I agree that's how I thought I would do it too - but I got a different response from FinCEN.
"FinCEN does not require the FI to identify the conductor for low dollar amounts. However, many institutions have systems in place to capture this data at the time of deposit just in case the aggregated transactions exceed the threshold. If the information is captured, then FinCEN expects it to be reported."
Per the FinCEN rep, "once any business entity has been captured on a CTR, the FI is required to aggregate and report ALL additional cash transactions transacted on the same business day, regardless of the conductor. Her specific guidance to the below scenario:
1. John Doe conducts the following transactions simultaneously that total $11,500
a. $4,500 cash deposit to benefit ABC Corp (EIN #12-3456789),
b. $4,000 cash deposit to benefit MNO, LLC (EIN #98-7654321),and
c. $3,000 cash deposit to benefit XYZ & Associates (EIN #34-5678912)
2. CTR is created for $11,500 with John Doe as conductor and the three business entities are identified as benefiting from the funds deposited
3. Later the same day, Michael Smith conducts the following two transactions simultaneously that total $750
a. $500 cash deposit to benefit ABC Corp (EIN #12-3456789), and
b. $250 cash deposit to benefit XYZ & Associates (EIN #34-5678912)
Part I for John Doe ($11,500) – 2b. Person conducting transaction for another
Part I for Michael Smith ($750) – 2b. Person conducting transaction for another
Part I for ABC Corp ($5,000) – 2c. Person on whose behalf transaction is conducted
Part I for MNO, LLC ($4,000) – 2c. Person on whose behalf transaction is conducted
Part I for XYZ & Associates ($3,250) – 2c. Person on whose behalf transaction is conducted
Part II #25 Total Cash In - $12,250"
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My opinions are my own, and not that of my employer.