Most writers run into this problem at one time or another. Thousands of books and published each year, with their own plot, so sometimes it seems like every idea in the world is taken.
Even if you come up with a new idea, when you sit down to write it, it starts to follow book you've read. Or the plot elements are the same. Or setting is the same. Or the characters act alike. Or...
The question is:
What makes your story different? And how can you make that evident in the story?
I've run into this problem before. When I finished the rough draft of my book The Golden Pegasus, I sent it out to several people. Almost everyone liked it, but one of the main responses was "this book is too much like ___". I struggled for a while trying to think of how I could make it different. I knew my idea was different. My main character was different and her challenges in life were different. The setting was a different, but there were a few details that kept it from being completely my own story.
But before you can make a story different from what people think it is similar to, you need to do a few things.
1. Re-read the book that your story is being compared to. Find how it is alike your story and why.
2. Identify what needs to be changed in order to make your book completely unique. Then change it.
3. Don't be afraid to change the plot or setting or characters in order to make your book stand on its own, without others' ideas influencing it.
4. It's always good to have someone else (besides you) read over it and tell you what they think. Truth is, you'll always find how your book is different. Others reading it will probably find how it is similar. Critique can be hard to handle, but it's always valuable.
Most of all, keep writing. Some ideas might not be the best, but more ideas will come. Comment and let me know how you try to make your idea original and unique :)