Significance Symbioses are evolutionarily and ecologically widespread, yet we lack a robust understanding of their origins, losses, and macroevolutionary consequences. We traced the evolution of partner choice and phenotype in lichens—a classic model of symbiosis—and revealed shifts among symbiont groups and phenotypic evolution. Symbiont switches broadly coincided with the convergent acquisition of similar partners by divergent clades. Fungi abandoned the lichen habit far earlier than previously understood, and subsequently reacquired it with algae that have frequently facilitated independent fungal transitions to lichenization. Finally, diversification in lichenized fungi was not strictly modulated by partner choice or phenotype, and differed from other fungi, suggesting complex and variable dynamics within lichen fungi and across fungal nutritional modes.