I live in Wisconsin, my company is based out of Wisconsin. It is an internet company. I plan on moving to California to finish schooling. I had hopes that they will let me work from home, while living in California. I was wondering what sort of tax implications could get held up in this process or possibility. State, Federal, etc.

Any help is greatly appreciated, I just want to be covered on all ends when I ask my employer and have as many point/counterpoints as I can in hopes to secure a job I can easily maintain while finishing my degree.

The key as to which state tax you pay rests with WHERE you are working.

If you work and live in Wisconsin, you pay Wisconsin state taxes.

If you work and live in California, you pay California state taxes.

You need to make sure your employer is aware of this, so that he can open a withholding account in California and start withholding California state income taxes (and probably state disability and unemployment taxes as well) from your salary.

Good luck!

If you are present in a state, then you must report income earned during that period to that state.

You must also report your worldwide income for the year to your resident state.
Read about taxes involving two or more states: Your U.S. Tax Return: Working or Living in Two or More states