Well first off all I would like to say that I did both. I'm a black belt in Judo and a blue belt in BJJ.
What mostly the difference is of the two is the primary goal. A BJJ fighter mostly comes from a defensive position, when a bjj blackbelt is taken down he can work of his back and is even more dangerous then when he has top position.
But Judo is different, Judo focusses more on taking your enemy down, secure dominant position and submit him. But since Judoka's are used to other guys trying that with them it useally provides them with great takedown and submission defence, but not so much with attacking of their backs, which is what BJJ guys are specialised in.
I think as an MMA fighter you should know both, since you want to be dangerous of your back, but also have those great takedowns and takedown defence, I mean, with a well executed hip or shoulder throw you can seriously hurt an enemy.