The purpose of the present paper is to introduce two notions of conditional entropy of a finite commutative hypergroup $\mathcal{K}$, one of which is associated with the normalized Haar measure of $\mathcal{K}$ and the other is associated with the canonical state of $M^b({\mathcal{K}})$ which is a $*$-algebra consisted of all measures on $\mathcal{K}$. For a subhypergroup or a generalized orbital hypergroup, the dual relations of these conditional entropy are discussed. Moreover, it is shown that the structures of hypergroups are characterized by these entropy.