Endosymbiosis is a universal relationship in nature, in which the symbiont is tightly integrated into the host and alters the host’s ecological niche and evolutionary trajectory. However, endosymbiosis can be easily disrupted by stress, which raises concerns about holobiont (symbiont plus host) persistence with global climate change, because massive endosymbiosis breakdown could have severe ecological consequences. The hologenome theory proposes that the symbiont and the host jointly determine the holobiont phenotype, and so rapid holobiont phenotype alteration can be achieved through changes in symbiont composition via strain acquisition, adaptation or acclimation. Previous studies have confirmed that switching symbionts can change holobionts’ stress tolerance, yet the relative roles of the symbiont and the host in controlling the holobiont phenotype are unclear as is whether symbiont adaptation or acclimation alone could allow holobionts to persist in stressful environments. My thesis addressed factors affecting stress tolerance of the holobiont green hydra (Hydra viridissima) from both the symbiont (green algae) and the host (hydra) perspectives, and experimentally explored how manipulations of the symbiont or the host alone could alter holobiont stress tolerance. Furthermore, I used agent-based modeling to simulate the holobiont adaptation via symbiont adaptation. My experimental results showed unequal contributions of the host and the symbiont to holobiont stress tolerance, with the host playing a dominant role. Furthermore, I detected positive transgenerational effects in the host. Although host traits are usually overlooked in holobiont studies, my studies suggest they are equally or even more important in determining holobiont stress tolerance. On the other hand, symbiont adaptation or acclimation provides the holobiont an extra route to acquire stress tolerance if the host fails to acquire it directly, and such acquired stress tolerance can be inherited. In addition, my experiments proved the feasibility of altering holobiont phenotypes by symbiont manipulations in vivo. Simulations further demonstrated that holobionts with either vertical or horizontal symbiont transmission are able to evolve solely through adaption of the symbiont. These findings support the hologenome theory and have implications for forestry, agriculture and conservation by providing insights into the determination and management of holobiont stress tolerance.