Sounds like an easy question, until you start realizing how many elements are in your book. It may be science fiction, but it may have romance, air pirates, and zombies. What would you call it, horror, sci-fi, romance, or steampunk? There are many things to consider.
First and foremost is, what is the heart of the story? Or rather, what is the strongest element in the book, the driving force. Is it the love story? The mystery? The adventure? Or is the main theme a fantasy world, futuristic, apocalyptic? That will help you determine the main genre. Also, think of where you might find it on the shelf in a bookstore. What are some comparable books? Where are they shelved? If you aren't sure, think about the type of readers that your book will attract. What do you like most about your book? The romance, the intricate fantasy world, forward thinking machines, adventure? These elements are found in books that are shelved in certain genre sections. That will help give you an idea of where to start.
Don't worry about all the crazy sub genres you hear about out there. They are enough to leave you reeling in confusion. Find the heart of your book and you will have found the genre. And find it you must, for if you do not know the heart of your book, how can anyone else?