Shiva was terribly afraid of the dark when she was younger. She had a lot of confidence issues . . . took me awhile to get her to realize that, barring the bear (that Bimmer took on ), she was the worst thing out there, as long as she didn't hare off after a pack of coyotes on her own.
Sal gets a little spooked at night when we go to visit my family out in the "country". When he goes outside at night for the first couple of times in the country he is kinda wary until his eyes adjust, then he is fine.
Night time in the city is different as street lights keep if from actually being dark. If we spend a day or two in the country then he seems to get over this "wariness".
Athena spent the first 3 years of her life living in the "country" so she doesn't seem to have this problem.
Well first thing I would do is have his eyes checked. After you know that a medical problem is not present, then you can work on it from a behavioral point. These tests are not done by a regular vet, but your vet can refer you to a doctor that can.
Our previous dog, Coco (Chesapeake Bay Retriever) would not walk up this one street in our old neighborhood at night. He would walk up the street a little ways and then STOP. You couldn't get him to budge. We never had a problem during the day though. There was a house at the end of that street where a guy committed suicide. I wonder if that had anything to do with it...