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If you are using TurboTax online, you will each need separate accounts, if you chose to file as Married Filing Separately (in lieu of Married Filing Jointly), although you can share the same email account during the registration process.
On the other hand, if you use any of the TurboTax desktop software products, then you can both share the same program for separate MFS tax returns. For that reason and depending on your circumstances -- which federal program version (e.g. Deluxe, Premier, etc.) you require based on the tax forms you need to file -- you may find it more cost-effective to use the desktop software rather than TurboTax online. This will be further true if you need to file a state tax return(s) as well.
With TurboTax online, each account is charged separately for the federal and accompanying state return. With TurboTax desktop, you only pay for the federal program just once. The federal desktop program also includes a single state download. If a second state download is required for a particular taxpayer situation, then again this extra state only needs to be purchased once, in contrast to TurboTax online and separate accounts.
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