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Peer-to-Peer (P2P) applications have witnessed an increasing popularity in recent years, which brings new challenges to network management and traffic engineering (TE). As basic input information, P2P traffic matrices are of significant importance for TE. Because of the excessively high cost of direct measurement, many studies aim to model and estimate general traffic matrices, but few focus on P2P traffic matrices. In this paper, we propose a model to estimate P2P traffic matrices in operational networks. Important factors are considered, including the number of peers, the localization ratio of P2P traffic, and the network distance. Here, the distance can be measured with AS hop counts or geographic distance. To validate our model, we evaluate its performance using traffic traces collected from both the real P2P video-on-demand (VoD) and file-sharing applications. Evaluation results show that the proposed model outperforms the other two typical models for the estimation of the general traffic matrices in several metrics, including spatial and temporal estimation errors, stability in the cases of oscillating and dynamic flows, and estimation bias. To the best of our knowledge, this is the first research on P2P traffic matrices estimation. P2P traffic matrices, derived from the model, can be applied to P2P traffic optimization and other TE fields.