In the context of the supersymmetric unification model in which the massless sector contains extra particles beyond those in the minimal supersymmetric standard model, we obtain mixings between quarks (leptons) and the extra particles which are closely intertwined with Yukawa hierarchies. With the assumption that the unification gauge group $G$ includes $SU(2)_R$, it is shown that the non-trivial texture of the CKM matrix originates from the extra-particle mixings. The CKM matrix of quarks emerges as a consequence of the mixings between the down-type quarks and colored Higgses, both of which are $SU(2)_L$-singlets. On the other hand, the CKM matrix of leptons is due to the mixings stemming from the seesaw mechanism with the hierarchical Majorana mass matrix of right-handed neutrinos.