Metapopulations persist when local populations are rapidly recolonized following local extinctions. Such persistence requires asynchrony; simultaneous crashes of all populations would leave no source of recolonization. We show theoretically and experimentally that catastrophic population extinctions themselves can promote metapopulation persistence, by preventing spatial synchrony and thus enhancing recolonization. We refer to this behaviour as the ‘spatial hydra effect’: as with the mythical hydra that grows two new heads when one is removed, extinctions can increase recolonization. The effect is robust, occurring in a wide range of theoretical models exhibiting cyclic or quasi-cyclic population dynamics. In a laboratory microcosm experiment using cyclic protist predator–prey metapopulations, catastrophic perturbations wiping out populations but leaving the patch otherwise unchanged increased metapopulation persistence when high dispersal rates would otherwise have led to spatially synchronous extinctions of all populations. We discuss several candidate examples of the spatial hydra effect in nature.