So, my employer informs me today that as i worked in two places last year (my present place being for the last 3 months) that i owe 16,500baht in TAX for the 2009 year.

They have told me the 'worst case scenario' is that my WP and visa will not be renewed in November 2010.

I plan to leave Thailand in September this year.

Are they right saying that is the 'worst case scenario??'

Obviously not.

So enlighten me?

What would the employee cares you owe taxes. Are they asking you to pay them the taxes? You have to file for taxes yourself and it depend on all you income during the year. I would let an accountant to take care of this

Take the paperwork your employers gave you and someone at the revenue office will help you fill out Form 91. They'll tell you if you owe anything, and collect it there.

If you pay your taxes, there shouldn't be a problem unless you don't meet the minimum amount for your nationality.