Studying how island biotas evolve and are dynamically shaped by interactions between resident species, their immediate environments and neighboring continental communities have provided basic understanding of ecological and evolutionary processes operating in these ecosystems. However, it remains to be seen how this knowledge applies to biodiverse groups such as lichens since these have been subjected to less scrutiny. To address this, my dissertation implemented integrative taxonomic approaches to shed light on factors that are crucial for the evolution of species and communities of lichenized fungi in tropical islands, specifically those from the Caribbean region. Chapter 1 emphasized using a phylogenetic framework based on multi-locus data from the lichen genus Sticta in Puerto Rico to reconstruct evolutionary origins and better quantify species richness within islands. We found that Puerto Rico hosts 16 species, eight of which I described as new. The group also exhibited a 69% degree of inferred endemism and formed polyphyletic assemblages, hinting at multiple colonization events over evolutionary time. Chapter 2 focused on reconstructing the evolutionary history of Caribbean Sticta and elucidating patterns of taxonomic and phylogenetic turnover between islands. To this end, I assembled a multi-locus dataset with representative taxa from these islands and other regions, performed macroevolutionary analysis, and estimated taxonomic and phylogenetic beta diversity indices for island-level communities. Ancestral range reconstruction analysis confirmed that most Caribbean species derived from South American ancestors, which first colonized the region nearly 19 Mya. No changes in diversification rates were detected as a result of range expansion to the Caribbean. Phylobetadiversity analysis, on the other hand, showed that taxonomic and phylogenetic turnover was most strongly correlated with variation along environmental gradients. The presumably high diversity of endemic species restricted to high elevation areas in Hispaniola and Jamaica likely underlies high dissimilarity detected between these communities and those from Puerto Rico and the Lesser Antilles. In Chapter 3, I combined phylogenetic methods with tools for visualization of population structure to revise the phylogeography of Cladonia sandstedei, a putative Caribbean endemic that shares parts of its range with the morphologically similar, but chemically different species C. subtenuis. This analysis was based on genome-wide data (RADseq) obtained for the southeastern US and Caribbean populations of both species. A major continental clade that showed a poor correlation between chemistry and phylogenetic structure was recovered, suggesting that chemical traits underperform for species discrimination purposes in this group. Strongly divergent island-level clades contrasted with poor separation between an inferred continental population and Jamaican individuals of both species, further hindering clarification of phylogeographic patterns. Cuban and Puerto Rican populations might deserve taxonomic recognition at the species level. Altogether, these projects represent the first attempt to characterize evolutionary events and processes that have shaped species diversity and phylogeographic patterns of lichens in this important biogeographic region. As such, my work ultimately highlights salient features that distinguish lichen evolution in tropical island systems.