The thallus anatomies of three common species of Canoparmelia and three species of Crespoa were compared to establish the characteristics that inform taxonomic studies and support distinctions between the two genera. Samples were processed using protocols developed for both morphological and anatomical studies. The anatomical studies revealed significant differences in the cortex and algal layer, supporting the distinction between Canoparmelia and Crespoa. The medullar arrangement in two strata found in Canoparmelia texana and Crespoa scrobicularis also proved to be an important distinctive characteristic for these species. Moreover, this study showed that the characteristics of the upper and lower cortex support the recent combination of Canoparmelia scrobicularis in Crespoa.