The roots of a polynomial in x are the values of x that, when we evaluate the polynomial at those values, we find 0. Think of it this way: there are two "0"s in the word "root." Fine, they're actually "o"s, but we won't tell anybody if you don't.
The polynomial x2 - 9 is 0 when evaluated at x = 3 or x = -3.
This means 3 and -3 are the roots of the polynomial x2 – 9.