In a great novels, there are many themes. So, I am sure that there will be differences of opinion. However, in my opinion, the main theme of the book is the duality of humanity. In other words, all people have two sides. This comes out very strongly in the final chapter when the relationship of the two men in title of the work becomes clear. At one point Dr. Jekyll confesses: "man is not truly one, but truly two." As the story unfold this becomes all to evident.
A variation of this theme could a bit darker. Man is not dual, but actually much darker. Mr. Hyde is emblematic of this as he takes over more and more and his deeds are far more base than what animals do, as he takes delight in harming people for the sake of harming them. If this is a theme, then the theme is one of human depravity.