I bought a 2001 Dodge Durango 5.9 and it only had keys no key fob. In the manual it says how to program a new key fob if you already have one, problem is I don't. So how would i program it?

 

You buy a new one from any given site on the internet and program it. Programming is a very easy process and you can do it yourself inside the Durango if you have an existing key fob but if not you will have to go to a dealership and I believe it's something like $40 to program it there.

Here's a couple of sites to check remotes out:
http://www.remotesandkeys.com/Produc...ductCode=3110A
http://www.keyless-remotes.com/dodge...e:2001:Durango
https://www.ikeyless.com/vehicles/Do.../2001/1000038/

 

since you dont have any key fobs you will have to take it to the dealer to have the first one programmed.