Anisotropies exist in many sedimentary rocks, particularly in naturally fractured reservoirs, causing horizontal stress anisotropies. Case studies indicate that when a rock formation contains high dip-angle fractures or contains horizontal factures (e.g. bedding planes), it has very distinguished horizontal stresses. In these cases, the conventional isotropic method for estimating horizontal stresses may give erroneous results. Using the theory of anisotropy, horizontal stresses in the vertical transverse isotropy (VTI) and horizontal transverse isotropy (HTI) models are derived for determining in situ stresses in naturally fractured rocks. Comparing with the isotropic model, the VTI model predicts a higher minimum or maximum horizontal stress, which is suitable for shales. In contrast, the HTI model gives a lower minimum stress than the isotropic model. A combined model based on the VTI and HTI models is proposed for estimating the minimum horizontal stress in a naturally fractured formation containing natural fractures with different dip angles. Measured data in the Xujiahe gas reservoir in China reveal that the minimum horizontal stresses and formation breakdown pressures decrease as the fracture dip angles increase, which is consistent to the derived HTI model. Natural fractures can result in a decrease of the minimum horizontal stress by up to 3 MPa/km and a reduction of the formation breakdown pressure by up to 10 MPa/km in the studied area. Combining the proposed anisotropic model to the measured data of natural fractures and horizontal stresses, the assessment of in situ stresses and their impact on hydraulic fracturing are proposed. Case study demonstrates that the proposed model gives a good prediction of the minimum horizontal stresses in the naturally fractured reservoir.