In this paper a systematic study of the orthogonal polynomial solutions of a second order partial difference equation of hypergeometric type of two variables is done. The Pearson's systems for the orthogonality weight of the solutions and also for the difference derivatives of the solutions are presented. The orthogonality property in subspaces is treated in detail, which leads to an analog of the Rodrigues-type formula for orthogonal polynomials of two discrete variables. A classification of the admissible equations as well as some examples related with bivariate Hahn, Kravchuk, Meixner, and Charlier families, and their algebraic and difference properties are explicitly given.