Numerous distinct clades of lichen-forming fungi have independently specialized as foliicolous colonists of living leaves in the humid tropics and subtropics. Because of technical difficulties, the anatomy of their minute crustose thalli has not been compared in detail. In the present study, we applied SEM-BSE imaging to sectioned blocks of embedded thalli representing six lecanoralean taxa of foliicolous lichen-forming fungi with unicellular green algal partners. We compared our observations with those obtained in a previous study of foliicolous Gomphillaceae (Ostropales), which utilize a similar type of algal partner. The upper surface of the thalli was a mostly continuous layer of mycobiont hyphae of typical diameter, unlike the largely acellular epilayer found previously in the foliicolous Gomphillaceae. Byssoloma leucoblepharum was exceptional in lacking a covering layer altogether. Thalli were essentially unstratified, with algal symbionts not confined to any distinct layer. Whereas the prothallus of foliicolous Gomphillaceae was derived from the overlying epilayer, in the lecanoralean taxa examined here the prothallus was derived from hyphae continuous with either the upper surface of the thallus or the lower surface, or both. This finding suggests that the prothallus of lichen forming fungi may represent structures of developmentally different origins in different taxa.