What This Letter Means

Letter 539 comes out of an IRS correspondence audit of a duplicate filing. Your Social Security number appeared twice for the same year: once as the primary filer on a separate return (single, head of household, or married filing separately) and once as the spouse on a joint return.

Before this letter you likely got Letter 31C asking which return was valid, and then an audit letter asking for information. Letter 539 is the 30-day letter. It proposes that the joint return is the return of record and that the separate return be combined into it. A Form 4549 report shows the proposed changes. If the returns are being combined, each spouse gets a letter at their own address of record.

Why the IRS Lands Here

The IRS generally keeps the joint return when the person on the separate return says the joint return is valid. A non-response can also keep the joint return, depending on which return was filed first and whether the separate return came in after the due date. If a valid joint return was filed and a separate return came in after the due date, the separate return doesn't replace the joint one. You can't switch from joint to separate after the due date.

The IRS compares the separate return's income and withholding to the joint return to make sure everything is reported. The separate return is removed when the case closes.

What to Do

  • Read the Form 4549 line by line. Check that income and withholding from your separate return were carried over correctly.
  • If you agree, follow the letter's instructions to sign and return the agreement form.
  • If you disagree, respond by the date on the letter. Explain why and send proof.

When the Joint Return Shouldn't Stand

Different facts lead to different results. If you never signed the joint return or your signature was forged, or if you weren't legally married, the IRS treats the separate return as the return of record instead. Send documents such as a divorce decree or a statement and evidence about the signature. Keep copies and use certified mail.

If you received Letter 539 and the joint return wasn't yours to sign, call us at (813) 229-7100.