Flood extent mapping plays a crucial role in disaster management and national water forecasting. Unfortunately, traditional classification methods are often hampered by the existence of noise, obstacles and heterogeneity in spectral features as well as implicit anisotropic spatial dependency across class labels. In this paper, we propose geographical hidden Markov tree, a probabilistic graphical model that generalizes the common hidden Markov model from a one dimensional sequence to a two dimensional map. Anisotropic spatial dependency is incorporated in the hidden class layer with a reverse tree structure. We also investigate computational algorithms for reverse tree construction, model parameter learning and class inference. Extensive evaluations on both synthetic and real world datasets show that proposed model outperforms multiple baselines in flood mapping, and our algorithms are scalable on large data sizes.