Many marine organisms host microalgal symbionts. Complex holobionts require adaptations to accommodate closely associated lifestyles when algae live within host tissues. Six categories of physiological adaptation in Symbiodinium-holobiont systems include pathways related to nutrient transfer, carbon concentration, nitrogen recycling, calcification, oxidative stress and cell-cell communication. Combining traditional physiological measurements with genomic and transcriptomic analysis informs hypotheses about underpinning mechanisms. As methods advance, large, next generation sequence data sets make broad comparative investigations possible. Integrating data from multiple partners provides insight on physiological solutions to cooperative living.