You can use TurboTax Online to file separate state returns, but we recommend you use the CD/Download software version to do this because you'll only need to pay for one TurboTax product (you can file up to five returns).
Here's detailed info on how to file as Married Filing Separate State Returns if you choose this option.
If you started in TurboTax Online, here's how to transfer your tax file to the desktop version.
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