Mississippi withholding tax Register, withhold, file, and reconcile

Get a withholding account

The DOR’s Publication 89-700 says employers must get a withholding account number from the department. You can apply online through TAP, the Taxpayer Access Point, at a local DOR office, or by calling the Registration Section at 601-923-7700. If you end up with two account numbers, tell the department.

The DOR withholding page also points to TAP for registration and online filing. Have your federal EIN, the Employer Identification Number from the IRS, before you start.

The Mississippi page on this site covers the rest of the first-hire setup, including unemployment tax with the Mississippi Department of Employment Security and the new-hire report.

The worker’s certificate: Form 89-350

Mississippi uses its own withholding certificate, Form 89-350. Publication 89-700 says you pick the table based on the worker’s Form 89-350 claim:

• Table A, Single.
• Table B, Head of Family.
• Table C, Married with a spouse not employed.
• Table D, Married with both spouses employed.

The federal Form W-4 does not tell you which Mississippi table to use. Collect both forms on the first day. What is withholding tax covers the federal form.

The 2026 rate and allowances

Publication 89-700 lists the rate schedule behind the 2026 tables:

Most employers use the tables or payroll software and never do this math. When a worker claims more exemptions than the table covers, the publication says to annualize: multiply pay to a yearly figure, subtract exemptions and the standard deduction, figure the tax, then divide by the number of pay periods.

Here is one example you can redo. A single worker earns $40,000 a year with no dependents. Subtract the $6,000 exemption and the $2,300 standard deduction, leaving $31,700. The first $10,000 is taxed at 0 percent. 4.0 percent of the other $21,700 is $868 for the year, or about $33.38 on each of 26 biweekly checks.

Filing and due dates

The DOR sets your filing frequency, monthly or quarterly, per Publication 89-700. Transient and seasonal employers file monthly. You file a return every period, even when no tax is due, and pay with the return.

The DOR withholding page says withholding returns are due on the 15th day of the month after the period. A date on a weekend or legal holiday moves to the next business day. So a December 2026 monthly return, or a fourth-quarter return, is due January 15, 2027.

Year-end: Forms W-2 and the annual return

The DOR withholding page sets these dates:

• Forms W-2 to employees by January 31.
• Forms W-2 to the DOR by January 31, paper or electronic.
• Forms 1099 to the DOR by February 28.

Publication 89-700 says a worker who leaves should get a Form W-2 within 30 days of the last day. It also says filing through TAP is required if you file 10 or more Forms W-2, 10 or more Forms 1099, use one payroll service for the whole year, or must file wage statements electronically with the federal government. Form 89-140, the Annual Information Return, is only for paper filers with fewer than 10 returns.

For 2026, January 31, 2027 is a Sunday. The DOR page moves a weekend due date to the next business day. Confirm on TAP, then file early. Year-end payroll checklist lines up the federal dates.

Bonuses and vacation pay

Publication 89-700 has its own supplemental wage rules. If you pay a bonus with regular wages, withhold on the total as one payment for the regular pay period. If you pay it separately, the publication gives two methods depending on whether you withheld from the worker’s regular wages, and both add the bonus to regular wages paid in the same year. Vacation pay for time off is regular pay. How bonuses are taxed covers the federal side, which works differently.

Workers who live or work out of state

The publication says nonresidents owe Mississippi withholding on wages for work done in Mississippi. If their main place of work is outside the state, figure the tax on total wages from the table, then multiply by the share of pay earned in Mississippi. A Mississippi resident who works in another state is subject to Mississippi withholding unless the other state requires its own.

Penalties

• 10 percent of the amount due for failing to withhold, filing late, or paying late.
• Interest of one-half percent a month on late tax.
• At least $250 for not filing the annual information return.
• $25 per Form W-2 not filed. $25 the first time and $500 each later time for not filing electronically when required.

The publication also says an employer who fails to withhold or pay is personally liable for the amounts.

Next step

Payroll software can withhold, file, and send Forms W-2 to Mississippi on plans that support the state. It uses the account number and Form 89-350 data you enter. The methodology page explains how we grade that split. Gusto is one plain link. Patriot is the other service on this site. The Mississippi page has the full checklist.