In this paper, the analysis for the performance of the discrete Fourier transform LMS adaptive filter (DFT-LMS) and the discrete cosine transform LMS adaptive filter (DCT-LMS) for the Markov-2 inputs is presented. To improve the convergence property of the least mean squares (LMS) adaptive filter, the DFT-LMS and DCT-LMS preprocess the inputs with the fixed orthogonal transforms and power normalization. We derive the asymptotic results for the eigenvalues and eigenvalue distributions of the preprocessed input autocorrelation matrices with DFT-LMS and DCT-LMS for Markov-2 inputs. These results explicitly show the superior decorrelation property of DCT-LMS over that of DFT-LMS, and also provide the upper bounds for the eigenvalue spreads of the finite-length DFT-LMS and DCT-LMS adaptive filters. Simulation results are demonstrated to support the analytic results.