Abstract The symbiosis between cnidarians and Symbiodinium algae (dinoflagellates) is the keystone responsible for the formation of the huge and important structures that are coral reefs. Today many environmental and/or anthropogenic threats compromise this tight relationship and lead to more frequent events of drastic loss of Symbiodinium pigments and eventually of algae themselves from cnidarians, better known as cnidarian bleaching. While the mechanisms underlying the collapse of the algae–coral symbiosis are progressively getting unraveled, the understanding of the mechanisms involved in the de novo infection of bleached cnidarians by Symbiodinium remains elusive. In this review, we describe the various steps needed to establish a stable symbiotic relationship between Symbiodinium and cnidarians. We review the mechanisms implicated in host–symbiont recognition and in symbiosome formation and persistence, with a special emphasis on the role played by lectins and Rab proteins. A better understanding of these molecular mechanisms may contribute to the development of strategies to promote post-bleaching recovery of corals.