Ivan86,
As I understand it, aikijutsu and jujutsu are very closely related. Aiki tends to lean more toward the principles of unbalancing the opponent before leveraging them, as opposed to jujutsu which is more concerned with the straight leverage action. Both can be very effective. Aiki tends to be more difficult to learn because it uses much less brute force and more subtlety. They are both old style Japanese arts. Please be aware that these are gross generalizations based upon my own knowledge. I am NOT an experienced practitioner of either discipline!
Another thing to be aware of is that there are a plethora of "Aikijutsu" and "Jujutsu" schools out there that are simply taking advantage of the popularity of the art. Right now it is aiki that is popular, so there are quite a number of bogus aiki schools around. In the 90s it was jujutsu, and in the 80s it was ninjutsu.
Just because someone says "we teach aikijutsu" doesn't necessarily make it so. Whenever you hear "aiki" these days, be sure and do lots of homework and ask lots of questions about the school and the instructor. If it's a legitimate school and a decent instructor, he'll welcome the fact that you are dedicated enough to the idea to research it, and will be happy to talk about his instructors. If he's bogus, he'll get upset when you ask about the history of the school and his qualifications to teach.
Good luck!