What is his seniority number?

The actual law for those who care
 

49 U.S. Code § 40116 - State taxation


Specifically subsection (f). Here it is. Read it in all its black and white glory. Look it up yourself if you don't trust an internet message board. If you don't understand what this means, consult your attorney or your tax professional.

(f)Pay of Air Carrier Employees.—

(1) In this subsection— (A) “pay” means money received by an employee for services.
(B) “State” means a State of the United States, the District of Columbia, and a territory or possession of the United States.
(C) an employee is deemed to have earned 50 percent of the employee’s pay in a State or political subdivision of a State in which the scheduled flight time of the employee in the State or subdivision is more than 50 percent of the total scheduled flight time of the employee when employed during the calendar year.


(2) The pay of an employee of an air carrier having regularly assigned duties on aircraft in at least 2 States is subject to the income tax laws of only the following:
(A) the State or political subdivision of the State that is the residence of the employee.
(B) the State or political subdivision of the State in which the employee earns more than 50 percent of the pay received by the employee from the carrier.



(3) Compensation paid by an air carrier to an employee described in subsection (a) in connection with such employee’s authorized leave or other authorized absence from regular duties on the carrier’s aircraft in order to perform services on behalf of the employee’s airline union shall be subject to the income tax laws of only the following: (A) The State or political subdivision of the State that is the residence of the employee.
(B) The State or political subdivision of the State in which the employee’s scheduled flight time would have been more than 50 percent of the employee’s total scheduled flight time for the calendar year had the employee been engaged full time in the performance of regularly assigned duties on the carrier’s aircraft.

https://www.law.cornell.edu/uscode/text/49/40116

BUMP

What to do if your employer says you need to pay tax where you where based despite your place of residence (that was on file with the company as another state) and the fact I operated more than 50% of my flights out of the state I was based at.

I also had TDY for two months in another state without even going to my base .

I already sent the tax law in this post to accounting department (which is a small company and they do a few different functions and to be honest I bet theyt are not the most experience or knowledge) but they don't see to agree with me and believe I should pay state tax where I'm based.

What type of operation?

135 on demand and schedule

Depending on your duties outside of flying you might well be required to pay state tax where you are based. You need to talk with a tax accountant. Where the company withholds is actually somewhat meaningless as you can just file a return to get all that money back. Your total time working however might be over 50% in that state.
The exemption to pay taxes on residence vice place of work also only applies to air carriers. Not sure a 135 operation falls under that definition. If it does not than where you reside is irrelevant.

Thanks for your reply

The company is talking to their CPA.

My wife's CPA is doing my taxes since we are filling joint and she has a complicated situation but he has no aviation experience. He told me that if I want to claim state tax in my residency instead of base the W2 would need to reflect that.

I’m not sure about the 135 under air carrier but could not find more information.

I also spent two months based in another state with company housing without coming to base at all

Thanks for your help

You are all going to jail.

"Did you really think we want those laws observed? We want them to be broken. You'd better get it straight that it's not a bunch of boy scouts you're up against... We're after power and we mean it... There's no way to rule innocent men. The only power any government has is the power to crack down on criminals. Well, when there aren't enough criminals one makes them. One declares so many things to be a crime that it becomes impossible for men to live without breaking laws. Who wants a nation of law-abiding citizens? What's there in that for anyone? But just pass the kind of laws that can neither be observed nor enforced or objectively interpreted – and you create a nation of law-breakers – and then you cash in on guilt. Now that's the system, that's the game, and once you understand it, you'll be much easier to deal with."

:eek::D