Hydra is a freshwater animal capable of full body regeneration. An excised tissue from a mature Hydra can fold into a hollow sphere, bringing the previous apical and basal sides together. A head organiser is established to act as a signalling centre for head formation, but the mechanisms underlying the regeneration of the head-foot body axis are still unclear. Here, Marko Popović, Kinneret Keren and colleagues investigate the relationship between tissue mechanics and morphogen signalling in axial patterning of the regenerating Hydra. Using live imaging, they observe that the supracellular actomyosin fibres are disoriented at two distinct foci of the regenerating tissue. These two topological defect sites eventually form the new head and foot. The authors find that multiple stretching and rupture events occur at the foci, and transient contractions of actin fibres focus mechanical strain at the defect sites. Additionally, under osmotic perturbation, previously shown to be associated with the reduction of Wnt expression, the formation of the head defect site is impaired, and an additional foot-like site is formed instead. Finally, they propose a mathematical model of a positive closed-loop feedback that incorporates fibre organisation, tissue strain and morphogen gradients to promote head organiser formation. Overall, the findings suggest Hydra regeneration is a dynamic self-organisation process that involves an interplay between morphogen signalling and tissue mechanics.