In this paper, parameter identification of two-dimensional continuous-time systems via two-dimensional modulating functions is proposed. In the proposed method, trigonometric functions and sine-cosine wavelets are used as modulating functions. By this, a partial differential equation on the finite-time intervals is converted into an algebraic equation linear in parameters. The parameters of the system can then be estimated using the least square algorithms. The underlying computations utilize a two-dimensional fast Fourier transform algorithm, without the need for estimating the unknown initial or boundary conditions, at the beginning of each finite-time interval. Numerical simulations are presented to show the effectiveness of the proposed algorithm.