There exist about 750 species of Cordyceps at present. A high price of natural Cordyceps and its lack in nature caused that the attention has been focused to its cultivation in laboratory conditions. The demand for this “fungus-parasite” is still quite high nowadays, as shown by the amount of commercial nutritional supplements. Phytochemical diversity has ensured that Cordyceps is used as an immunomodulatory and an antioxidant; it has anti-cancer, anti-inflammatory, anti-diabetic, antibacterial, anti-HIV effects. In the present study we focused on NMR and IR analyses of natural substances isolated from two species of Cordyceps: Cordyceps sinensis MFTCCB025/0216, MFTCCB026/0216 and Paecilomyces hepiali MFTCCB023/0216. Two types of rice substrates (Oryza sativa Indica and Oryza sativa Japonica) were used for cultivation. A total of five methanol extracts obtained by a reflux method of the ground mushroom were analysed. To determine the quality and quantity of the major chemical compounds, 1D and 2D NMR analysis has been used with 1H, 13C, COSY, NOESY, HSQC, HMBC and DEPT spectra. IR spectroscopy was chosen as a complementary analysis to determine functional groups. Linoleic acid, oleic acid and mannitol were identified as major compounds of the methanol extracts. Tyrosine, alanine, urea and the others biologically interesting substances were found as minor components.