Wildfires are one of the most destructive natural disasters that can affect our environment, with significant effects also on wildlife. Recently, climate change and human activities have resulted in higher frequencies of wildfires throughout the world. Timely and accurate detection of the burned areas can help to make decisions for their management. Remote sensing satellite imagery can have a key role in mapping burned areas due to its wide coverage, high-resolution data collection, and low capture times. However, although many studies have reported on burned area mapping based on remote sensing imagery in recent decades, accurate burned area mapping remains a major challenge due to the complexity of the background and the diversity of the burned areas. This paper presents a novel framework for burned area mapping based on Deep Siamese Morphological Neural Network (DSMNN-Net) and heterogeneous datasets. The DSMNN-Net framework is based on change detection through proposing a pre/post-fire method that is compatible with heterogeneous remote sensing datasets. The proposed network combines multiscale convolution layers and morphological layers (erosion and dilation) to generate deep features. To evaluate the performance of the method proposed here, two case study areas in Australian forests were selected. The framework used can better detect burned areas compared to other state-of-the-art burned area mapping procedures, with a performance of >98% for overall accuracy index, and a kappa coefficient of >0.9, using multispectral Sentinel-2 and hyperspectral PRISMA image datasets. The analyses of the two datasets illustrate that the DSMNN-Net is sufficiently valid and robust for burned area mapping, and especially for complex areas.