My 16 month old Rottweiler is marking his terrirory in the house. In the same spot, I haven't caught him ever in the act and when I show it to him he cowers and runs outside. He is house broken and has a dog door. He is not neutered and has a 5 yr old retriever as a friend. The golden has live here for 6 months now.

Please get him neutered. That's why he's marking his territory, to be alpha over the younger dog. And please do not scold him or push his nose in it -- he honestly doesn't understand what he did. (As far as he knows, what he did is perfectly fine and natural!) He just knows you are angry, thus he cowers and runs outside.

Dog experts will show up and will advise you further.

Nope WG, your answer was perfect.

He needs to be neutered, that will help tremendously. I had an entire male here who used to mark in the house, he even marked on my bed on a regular basis.
He had the snip at about 12 months of age and we haven't had a problem since.

I'm not saying it is a miracle cure, most dogs still require training but it certainly will help.

When you find the pee and show it to him he does not understand, he wouldn't even realise you are showing him the pee, like WG said all he understand is you are angry and being mean to him for no reason.
When mine have accidents I just calmly clean it up and spray an enzyme product on the area.

If you don't catch him in the act he has no idea what you're talking about.

Why does he cower from you? Do you strike him?

I don't hit my dogs, at all, but they know when they have done something wrong. Dogs know that the mess in the house is bad and upsetting you, but not the actual act of doing it. They can pick up on emotions even if you aren't expressing yourself by hitting or yelling. If he is not neutered, he will continue to mark his territory, especially seeing as there is a new dog in the house.

Is there some reason you haven't neutered? Your dog will be much happier and healthier after being neutered.