The road to recovery of a deteriorated system is often different, and fraught with more barriers, than the path to the system's deterioration. This phenomenon is called hysteresis, and is inherent to systems presenting alternative stable states. In such systems, the stability of a given state is the product of positive feedback loops. A broad range of natural systems have been predicted to show hysteretic behaviour, but hysteresis has so far only been unambiguously demonstrated at cellular or metabolic levels, not yet at the population or ecosystem level. To extend our understanding of hysteresis at the population level, we performed an experiment on light-stressed cyanobacteria and found hysteresis between alternative stable states. Furthermore, during the experiment, the cyanobacteria adapted physiologically to high light levels, and deviated from their theoretically predicted pathway of hysteresis, therewith also avoiding extinction. Our experiment confirmed that a population that loses resilience due to deteriorating external conditions can show a delayed – hysteretic – recovery-response when conditions are improved. This population-level study also indicates that the slowness of these systems may obscure the true state they are in, which is important to factor into ecosystem monitoring. Additionally, we show that adaptation can drastically alter the systems’ predicted behaviour to ecosystem management. Flexibility of species and slowness should, therefore, be included in the monitoring and prediction of ecosystem responses to environmental changes.