Hypericum lydium Boiss. is a perennial plant of the Hypericaceae family, which has been used in particular to treat depression. The aim of this study was to determine in vitro antioxidant, antimicrobial activities, anticholinesterase (acetylcholinesterase (AChE)/butyrylcholinesterase (BChE)), antidiabetic activities (α-glucosidase/α-amylase) and Tyrosinase inhibitor activity of methanol and water extracts of H. lydium. Also, gene expression has been evaluated in the shoot and root by microarray technology. So, in general, the purpose of this study is to study the active molecules such as antioxidant, antimicrobial, antidiabetic, enzymes and genes in the plant, which is the first to be reported. The experiments were conducted in a completely randomized design with three replications. In addition, gene expression was compared in the shoot and root parts. Expression profiling was carried out by microarrays. According to the results, the highest chemical components were determined in methanol extract rather than water extract. There was a difference between the obtained components. While the highest antioxidant activity was determined from the methanol extract of plant herbs for DPPH Free Radical Scavenging Activity, antioxidant activity was the same in both methanol and water extracts using the ABTS method. The methanol extract demonstrated stronger anticholinesterase (AChE and BChE) and α-amylase inhibition activity. This study was complemented by the detection of antioxidant activity and some enzyme inhibition activity in the methanol extract. Microarray showed 10,784 genes had significantly different expression in root and shoot. There was a positive effect of methanol extract in respect of different activities compared to the water extract. Gene expression showed that the number of expressed genes in the root was greater than the shoot.