Lichen as the typical symbioses, reproduction and dispersal strategies play a major role in shaping their population structure and photobiont diversity. Sexual reproduction strategy is common in lichenized fungi, which leads to a high lichen genetic diversity and a low photobiont selectivity. Whereas a rare myco-and photobiont co-dispersal sexual patterns in lichens whose mycobiont is sexually reproductive, provides a different insight to understand how lichen population structure is shaped. Individuals from Endocarpon (Verrucariaceae, Verrucariales, Ascomycota) are widely distributed in desert or high mountains with well-known stress tolerance, and implement a co-dispersal strategy that their ascospores are sprayed with photosynthetic algae. A total of 62 Endocarpon individuals and 12 related Verrucariaceae genera (Placidiopsis, Placidium, and Verrucaria) individuals, representing co-dispersal strategy and conventional independent dispersal mode were studied to explore the dispersal strategy impact on lichen population structures. These individuals were collected from six areas, spanning almost across China from north to south. Phylogenetic analysis revealed that Endocarpon, with a large-scale geographical distribution, showed an extremely high specificity of symbiotic associations with their photobiont, while the other genera showed different photobiont diversity. Furthermore, three types of group I intron at 1769 site have been found in most Endocarpon mycobionts, which showed a high variety of group I intron in the same insertion site even in the same species collected from one location. The current study suggested that the ascospore-alga co-dispersal mode of Endocarpon resulted in this unusual mycobiont-photobiont relationship; also provided an evidence for the horizontal transfer of group I intron that may suggest the origin of the complexity and diversity of lichen symbiotic associations.