A linear transformation (LT) is characterized entirely by its action on a basis, since all other vectors can be made out of a linear combination of that basis. Thus, if you specify LT{basis vectors}, you've essentially told me how the entire LT works.
This information can be captured in a matrix. Thus, the matrix represents the LT. However, as mentioned above, what the matrix describes is where the basis vectors get mapped to. Since there are multiple possible bases, the matrix representation is not unique. The same LT described with respect to different bases gets captured as a different matrix.
In your case, the "matrix in the canonical basis" means that the LT is being captured as a matrix with respect to the canonical basis (i.e. the standard basis).