Abstract The spatial arrangement of tissues during development establishes regions of tissue-tissue interactions. While such interactions are prominent during gastrulation and organogenesis, how they guide morphogenesis remains unclear. Here, using Xenopus animal cap explants, we show that the coupling between epithelial and mesenchymal tissues is instrumental in robust axis elongation. We find that mesenchymal and epithelial tissues drive elongation hierarchically - the epithelium can elongate independently, while the mesenchyme requires the initial presence of the epithelium. The epithelial-mesenchymal boundary defines the direction of cell shape alignment and the axis of tissue elongation. Prior to explant elongation, epithelial cells align and elongate, a process that propagates into the underlying mesenchyme. These findings reveal how tissue boundaries can organize coherent axis elongation without external patterning cues, providing insights into the self-organization principles that guide embryonic morphogenesis.