The current longest reigning titleholder is Omar Andres Narvaez. He's the WBO world flyweight champion and has had it for more than 7½ years.
The runner-up is the WBA super world featherweight champion Chris John. He's had his title for about 6 years.
Bet you didn't know this.
I find it interesting, It would be nice to see a list of the top ten or twenty.
I do agree with jreckoning about the quality of opposition Narvaez had faced, but that is a benefit of being a wbo champion.