Lichens are a well-known source of bioactive metabolites with agricultural and pharmaceutical importance and have the potential for biotechnological and industrial applications. However, despite numerous studies on lichen secondary metabolite production, little is known about the biosynthetic gene clusters (BGCs) responsible for lichen metabolites production, largely due to the slow growth rate of lichens, their inability to produce metabolites of interest in axenic culture, and their recalcitrance to genetic transformation. For this reason, the primary goal of this paper is to develop a deeper understanding of the lichen BGCs and their involvement in the production of various metabolites. To do this, we first evaluated the antimicrobial potential of endolichenic fungi (ELF) and lichen substances against plant pathogens and observed that both ELF and lichen acids exhibited bioactivity against Clavibacter michiganensis var. michiganensis, a Gram-positive bacterium, and several other pathogenic fungi. Additionally, several compounds were identified in ELFs as potential metabolites responsible for their antimicrobial activity, confirming the significance of both ELFs and lichen substances as valuable sources of important secondary metabolites. Given the importance of lichen natural products, a more comprehensive understanding of their bioactivity requires a significant quantity of available metabolites. Thus, we investigated the production of lobaric acid in Stereocaulon alpinum and cristazarin in Cladonia metacorallifera. We analyzed the transcriptomic data, and identified a highly expressed BGC for each, which are likely responsible for lobaric acid and cristazarin production, respectively. Specifically, a non-reducing PKS (PKS 27) and a highly reducing PKS (PKS47) were identified for lobaric acid production, while a non-reducing PKS (PKS22) was linked with cristazarin production. The connection between cristazarin production and PKS22 was further supported by BGC sequence similarity network analysis and phylogenetic analysis demonstrating a close association between PKS22 and those involved in melanin production (PKS13, PKS14, PKS15). We also investigated the production of salazinic acid in Parmelia sp. KoLRI_050094 and identified PKS1 as the gene responsible for salazinic acid production. Since PKS1 is closely related to PKS23, responsible for 4-O-demethylbarbatic acid formation, we performed heterologous expression of sal2, sal3, sal5, and sal6 in a heterologous host containing atr1 gene and identified sal3 as the gene responsible for the depsidone formation. Specifically, the expression of sal3 in the heterologous host Ascochyta rabiei resulted in a successful conversion of the depside precursor 4-O-demethylbarbatic acid to a depsidone. Finally, the heterologous expression of sal6 in the opposite direction with sal3, was found to oxidize the alcohol group to an aldehyde group in the resulting depsidone compound. While we established the roles of sal3 and sal6 in depsidone biosynthesis, the functions of sal2, sal5, and the accessory genes related to lobaric acid and cristazarin production are still under investigation. In conclusion, this study provides a foundation for systematically linking lichen BGCs with their corresponding secondary metabolites. Given the plethora of lichen natural products, we confirm that the use of transcriptomic analysis, BGC sequence similarity network analysis, and phylogenetic analysis paves the way in unraveling the connection between BGCs and the novel metabolites of interest. Ultimately, this work provides important insights into the synthesis of depsides and depsidones, gene function, and metabolic diversity in LFFs which is a cornerstone to improve the biotechnological production of valuable natural products.