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I think that Jess had reasons to be jealous, Dean was much more aggressive towards Jess. He seemed always ready to fight Jess. I think that Jess was afraid that Rory might go back to Dean. Remember that Lorelai loved Dean, the town loved Dean (except Luke) so I think that he was afraid that Rory would try to live up to the expectations of her mother and the town. Especially after that Dean comment "...just friends, like you and Rory were just friends...", Jess had ample reasons to be jealous. Add in the fact that in Swan Song, Rory assumes that Jess had gotten into a fight with Dean.

So, I think that Jess had reasons to be jealous!!!

i tottly agree with rorymariano
and he had verey right to be jealous i mean the min he was gone she did went back to him even thought he was married

If anything Jess was the least jealous boyfriend of all of Rory's boyfriends. So I'd say his jealousy was justified because Dean had made it very clear he was still after Rory, and obviously there would still be some feeling still there, so Jess was probabaly just afraid she may go back to him. His jealousy only really flairs up when he hears Rory and Dean hung out from somewhere other then her, if Rory mentions it he's usual abit more calm.

I totally agree with CelestialDream :D. I think that his jealousy was justified and only came up when he had heared they had been together.