DNA sequencing techniques and molecular and phylogenetic analyses have developed rapidly over a short time, finding application in fields across biology and medicine. The field of lichenology is no exception, with hundreds of studies utilizing DNA sequences to reconstruct phylogenies and uncover the evolutionary histories of populations and species. Given the dramatic advancements of sequencing technologies, analytical techniques and computational capabilities, an assessment of trends in molecular lichen research is timely. We present a literature meta-analysis that reviews the existing published molecular and phylogenetic research using traditional (e.g., Sanger) and next-generation (e.g., Illumina) sequencing technologies. Specifically we (i) determine how molecular data have been applied to lichens thus far, (ii) document and discuss trends in sequence data application, (iii) examine taxonomic representation and biases at the family level, and (iv) outline avenues of future research as well as highlight areas where targeted study is urgently needed.