A machine learning algorithm that performs multifidelity domain decomposition is introduced. While the design of complex systems can be facilitated by numerical simulations, the determination of appropriate physics couplings and levels of model fidelity can be challenging. The proposed method automatically divides the computational domain into subregions and assigns required fidelity level, using a small number of high fidelity simulations to generate training data and low fidelity solutions as input data. Unsupervised and supervised machine learning algorithms are used to correlate features from low fidelity solutions to fidelity assignment. The effectiveness of the method is demonstrated in a problem of viscous fluid flow around a cylinder at Re ≈ 20. Ling et al. built physics-informed invariance and symmetry properties into machine learning models and demonstrated improved model generalizability. Along these lines, we avoid using problem dependent features such as coordinates of sample points, object geometry or flow conditions as explicit inputs to the machine learning model. Use of pointwise flow features generates large data sets from only one or two high fidelity simulations, and the fidelity predictor model achieved 99.5% accuracy at training points. The trained model was shown to be capable of predicting a fidelity map for a problem with an altered cylinder radius. A significant improvement in the prediction performance was seen when inputs are expanded to include multiscale features that incorporate neighborhood information.