The lichen Asahinea scholanderi (Llano) W.L.Culb. & C.F.Culb. (Cetrarioid clade, Parmeliaceae family) is a potent acetylcholinesterase and butyrylcholinesterase inhibitor. The aim of the present work is to identify the major bioactive compounds of Asahinea scholanderi and clarify how they could inhibit the enzymes acetylcholinesterase (AchE) and butyrylcholinesterase (BuchE). The HPLC study showed that the main secondary metabolites were alectoronic acid, α-collatolic acid. Molecular docking studies revealed that the binding energy values were -10.8 kcal/mol (with water) and -11.1 kcal/mol (without water) for alectoronic acid and -7.2 kcal/mol (with water) and -9.9 kcal/mol (without water) for collatolic acid in acetylcholinesterase. On the other hand, the binding energy values for the secondary metabolites of Asahinea scholanderi against butyrylcholinesterase were -6.2 kcal/mol (with water) and -6.6 kcal/mol (without water) for alectoronic acid and -5.5 kcal/mol (with water) and -6.7 kcal/mol (without water) for collatolic acid. Therefore, the molecular interaction between the major secondary metabolites of Asahinea scholanderi revealed that alectoronic acid exhibited strong interactions with both AChE and BuChE with and without water molecules in the binding site. These molecules should be further investigated as cholinesterase inhibitors for the prevention and treatment of Alzheimer’s disease.