The original version of the Gilligan's Island theme song was recorded by The Wellingtons.
According to "Here on Gilligan's Isle", the second (and third) season version of the song was performed by a group called The Eligibles.
User "supercat" asked in a comment on this question:
Do you know if the Wellingtons demanded a per-show royalty, or if there was some other reason they were used for the first season but not the second? Until I watched the show on DVD, I would have guessed the later theme started in a lower key; I was surprised to find the difference stems purely from the different singers' voices.
Why weren't The Wellingtons used for the later season recording(s)?
I just remember the lyrics changed at some point; they mentioned the professor and Maryann and then those two were replaced by the words "the rest".
that is completely wrong! It was "The rest" first then changed to "the Professor and Maryann" And it was because the viewers did not know who "the rest" was, and because it was two more people in the group they then included "the Professor and Maryann.