Hydra is an extremely long-lived genus of freshwater polyps with tremendous regeneration abilities. Here, we present genome sequencing data of six Hydra vulgaris single-cells (3 epithelial and 3 interstitial) and of eight related Hydra individuals. The data allows identification of heavily adapted and strongly conserved pathways / processes in the commonly used laboratory strain 105 at different evolutionary time scales. In addition, these data allow to estimate the somatic mutation rate in Hydra.