It is commonly observed that various types of defect structures, including dislocations, interfaces, grain boundaries, etc, can be generated accompanying with structural phase transformations. The types of the defects are not only associated with the symmetry of the parent and product crystals, but also dictated by the transformation pathway between the two crystals. In this work, we show that a hidden pathway can be discovered through crystal symmetry analysis in some popular material systems, e.g., iron-based alloys and titanium-based alloys, which results in the generation of characteristic types of defect structures during phase transformations. The defect generation through the hidden pathway is distinctively different from plasticity because it doesn’t require stress concentration as high as yield stress. Such an intrinsic connection between phase transformation and defect generation provides a theoretical foundation for crystallographic design of domain and defect structures in defect engineering.