Let $\mathcal{M}$ denote the Bose-Mesner algebra of a commutative $d$-class association scheme ${\mathfrak X}$ (not necessarily symmetric), and $\Gamma$ denote a (strongly) connected (directed) graph with adjacency matrix $A$. Under the assumption that $A$ belongs to $\mathcal{M}$, we describe the combinatorial structure of $\Gamma$. Moreover, we provide an algebraic-combinatorial characterization of $\Gamma$ when $A$ generates $\mathcal{M}$. Among else, we show that, if ${\mathfrak X}$ is a commutative $3$-class association scheme that is not an amorphic symmetric scheme, then we can always find a (directed) graph $\Gamma$ such that the adjacency matrix $A$ of $\Gamma$ generates the Bose-Mesner algebra $\mathcal{M}$ of ${\mathfrak X}$.