As part of a comprehensive study on lecideoid lichens in Antarctica, we investigated the photobiont diversity and abundance in 119 specimens of lecideoid lichens from 11 localities in the continental and maritime Antarctic. A phylogeny of these photobiont ITS sequences, including samples from arctic, alpine and temperate lowland regions, reveals the presence of five major Trebouxia clades in Antarctic lecideoid lichens. Two clades are formed by members of the T. jamesii and T. impressa aggregates but for all other clades no close match to any known Trebouxia species could be found in sequence databases. One genetically uniform and well-supported Trebouxia clade was found only in the climatically unique cold desert regions of the Antarctic (preliminarily called Trebouxia sp.URa1), where it is preferentially associated with the highly adapted Antarctic endemic lichen Lecidea cancriformis. Levels of genetic photobiont diversity differ slightly, but insignificantly among ecological regions of the Antarctic and do not decrease towards regions with more unfavourable ecological conditions. The genetic diversity of photobionts varies among mycobiont species. Most pairwise comparisons reveal that these differences are insignificant, probably due to the small sample size for most species. The Antarctic lichens studied here are predominantly not specific for a single photobiont species or lineage, except for Lecidella greenii and L. siplei. These two species are preferably associated with Trebouxia sp. URa2, although in the sampling areas of both species, a pool of several other photobionts is available. Lecidea cancriformis associates with the highest diversity of photobionts followed by L. andersonii.