A light microscopic and molecular analysis of photobionts in Ramalina and Cladonia from coastal habitats of Brazil is presented. A Bayesian phylogenetic analysis of ITS rDNA sequences suggests a Trebouxia lineage which is preferentially tropical in geographic distribution. This highly diverse clade also includes the morphological similar species Trebouxia higginsiae and galapagensis. Within the predominantly tropical clade of Trebouxia we distinguish several subclades, three of which are represented in our samples of Ramalina species. Since sexuality has not been recognized in coccal lichenised photobionts until recently, we cannot apply a biological species concept, but when compared with the sequence diversity between known species we conclude that several new species need to be described in this clade. The mutually exclusive presence of other Trebouxia lineages in temperate samples of Ramalina suggests an evolution towards higher selectivity in this genus. A strictly tropical lineage is not conspicuous in the photobionts of the genus Asterochloris sampled from Cladonia so far.