Is It Young Adult or Middle Grade?

Q. My 96,000-word manuscript features a 12 yr old and 11 yrs old protagonist, the themes are dark. Have been looking around and am unsure -- YA or mid-grade? Help!
- Marco

A. I think I can help. I just finished my first middle grade novel and, for a good while, I thought it was a young adult work. But then I did a lot of research to try and distinguish between the two juvenile categories.
First of all, your word count is way, way off. It's so off that an agent will see the word count and stop reading your query. MG novels run 20,000-40,000 words, while YA is 40,000-65,000 words.
The ages of your characters looks like it is MG. Protagonists there are usually 12-13. Someone once told me that readers like to enjoy a story where the protagonist is older, and in a situation they will soon be in. So for MG, where the readers are 9-12, they want to read about 13-year-olds, etc. For YA, where the readers are 11-14, they want to read about 16-year-olds or above.
As far as "dark themes" go, I can't help you because I haven't read the book. Dark themes are OK in MG, but avoid sex and drug use. It sounds to me like you still don't know what your book is, and need to do some more research (and then make lots of cuts!).

Update: Here is a comment from a writer - "The field of middle-grade fiction encompasses more than Magic Tree House-style chapter books. It's not uncommon for MG novels to run 60,000 to 100,000 words (Harry Potter, Percy Jackson, Artemis Fowl, to name a few popular examples)."

A. To me, these examples you list seem like big exceptions to the rule, and that word count mentioned seems pretty far off. So - I consulted Michelle Andelman, an agent wise to all things children's.
Michelle said that fantasy submissions are an exception to the rule and new writers can get away with a submission that maxs out at about 65,000 words, but a bigger word count is troublesome. However, that said, the 20,000-40,000 word count general range is still correct and should be followed if you want to give yourself your best shot with agents and editors.
There are always exceptions to every guideline in writing, but if you count on being the exception to the rule, you are setting yourself up for disappointment.