The symbiotic hydra Hydra viridissima has a stable symbiotic relationship with the green alga Chlorella . This hydra appears to cospeciate with the symbiotic alga, and some strains are known to have strain-specific host/symbiont combinations. To investigate the mechanism of the specificity between host and symbiont, we explored the effect of the removal or exchange of symbionts in two distantly related H. viridissima strains (K10 and M9). In the K10 strain, severe morphological and behavioural changes were found in symbiont-removed and symbiont-exchanged polyps. Interestingly, both polyps showed a similar gene expression pattern. The gene ontology (GO) enrichment analysis revealed that the removal or exchange of symbionts caused the downregulation of genes involved in the electron transport chain and the upregulation of genes involved in translation in the K10 strain. On the other hand, symbiont-removed and symbiont-exchanged M9 polyps showed modest changes in their morphology and behaviour compared with the K10 strain. Furthermore, the patterns of the gene expression changes in the M9 strain were quite different between the symbiont-removed and symbiont-exchanged polyps. Our results suggested that the regulation of energy balance is one of the crucial mechanisms for maintaining symbiotic relationships in green hydra, and this mechanism differs between the strains.