My wife didn't file taxes the last two years and was working. She has a refund for 15 but owes for 16. We've never filed jointly, what happens if we file jointly this yr?

[Jimesa]

There is a possibility that any refund you receive on a joint return could go towards her past due debt. She should file her 2015 & 2016 returns immediately and request a payment plan with the IRS if needed, to prevent more drastic measures being taken. Typically the IRS will grant payment plans fairly easily. You all could also consider filing as "Married Filing Seperately" until she clears her past tax obilgations. Please see the below links for some helpful information:

Is it better for a married couple to file jointly or separately?

https://ttlc.intuit.com/replies/3288477

Additional Information on Payment Plans

https://www.irs.gov/payments/payment-plans-installment-agreements